id stringlengths 13 13 | task_type stringclasses 6
values | pipeline stringclasses 1
value | difficulty stringclasses 3
values | num_hops int64 1 5 | question stringlengths 94 258 | context stringlengths 41 511 | reasoning_chain dict | answer stringlengths 1 511 | modalities listlengths 1 3 | modality_data listlengths 1 5 | evidence listlengths 1 5 | metadata stringlengths 49 912 | path_confidence_score float64 0.61 1 | choices listlengths 4 4 ⌀ |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
no_dise_00435 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in FGFR1 classified as Pathogenic or Likely Pathogenic for Hypogonadotropic hypogonadism. | NM_023110.3(FGFR1):c.670G>C (p.Asp224His) VARIANT_IN_GENE FGFR1 → NM_023110.3(FGFR1):c.670G>C (p.Asp224His) VARIANT_HAS_CLINICAL_SIGNIFICANCE Hypogonadotropic hypogonadism | {
"steps": [
{
"hop": 1,
"source_node_id": "FGFR1",
"source_node_type": "GENE",
"source_node_label": "FGFR1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_023110.3... | NM_023110.3(FGFR1):c.670G>C (p.Asp224His) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"FGFR1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"FGFR1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_023110.3(FGFR1):c.670G>C (p.Asp224His)",
"text": "NM_023110.3(FGFR1):c.670G>C (p.Asp224His) VARIANT_IN_GENE FGFR1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hypogonadotropic_hypogonadism",
"text": "NM_023110.3(FGFR1... | {"gene": "FGFR1", "disease": "Hypogonadotropic hypogonadism", "pathogenic_variants": ["NM_023110.3(FGFR1):c.729C>A (p.Tyr243Ter)", "NM_023110.3(FGFR1):c.1716C>G (p.Tyr572Ter)", "NM_023110.3(FGFR1):c.1029G>A (p.Ala343=)", "NM_023110.3(FGFR1):c.670G>C (p.Asp224His)"]} | 0.921954 | null |
no_dise_00294 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRAF classified as Pathogenic or Likely Pathogenic for BRAF-related disorder. | NM_004333.6(BRAF):c.722C>T (p.Thr241Met) VARIANT_IN_GENE BRAF → NM_004333.6(BRAF):c.722C>T (p.Thr241Met) VARIANT_HAS_CLINICAL_SIGNIFICANCE BRAF-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004333.6(B... | NM_004333.6(BRAF):c.722C>T (p.Thr241Met) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRAF\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRAF\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_004333.6(BRAF):c.722C>T (p.Thr241Met)",
"text": "NM_004333.6(BRAF):c.722C>T (p.Thr241Met) VARIANT_IN_GENE BRAF",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:braf_related_disorder",
"text": "NM_004333.6(BRAF):c.722C>T (... | {"gene": "BRAF", "disease": "BRAF-related disorder", "pathogenic_variants": ["NM_004333.6(BRAF):c.1502A>C (p.Glu501Ala)", "NM_004333.6(BRAF):c.1403T>C (p.Phe468Ser)", "NM_004333.6(BRAF):c.722C>T (p.Thr241Met)"]} | 0.921954 | null |
no_dise_00185 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in FAT4 classified as Pathogenic or Likely Pathogenic for Autosomal recessive FAT4-related disorders. | NM_001291303.3(FAT4):c.7504G>T (p.Glu2502Ter) VARIANT_IN_GENE FAT4 → NM_001291303.3(FAT4):c.7504G>T (p.Glu2502Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Autosomal recessive FAT4-related disorders | {
"steps": [
{
"hop": 1,
"source_node_id": "FAT4",
"source_node_type": "GENE",
"source_node_label": "FAT4",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001291303.... | NM_001291303.3(FAT4):c.7504G>T (p.Glu2502Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"FAT4\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"FAT4\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_001291303.3(FAT4):c.7504G>T (p.Glu2502Ter)",
"text": "NM_001291303.3(FAT4):c.7504G>T (p.Glu2502Ter) VARIANT_IN_GENE FAT4",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:autosomal_recessive_fat4_related_disorders",
"text"... | {"gene": "FAT4", "disease": "Autosomal recessive FAT4-related disorders", "pathogenic_variants": ["NM_001291303.3(FAT4):c.7504G>T (p.Glu2502Ter)"]} | 0.921954 | null |
no_dise_00345 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in FGFR1 classified as Pathogenic or Likely Pathogenic for Autosomal recessive FGFR1-related disorders. | NM_023110.3(FGFR1):c.1889T>G (p.Leu630Arg) VARIANT_IN_GENE FGFR1 → NM_023110.3(FGFR1):c.1889T>G (p.Leu630Arg) VARIANT_HAS_CLINICAL_SIGNIFICANCE Autosomal recessive FGFR1-related disorders | {
"steps": [
{
"hop": 1,
"source_node_id": "FGFR1",
"source_node_type": "GENE",
"source_node_label": "FGFR1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_023110.3... | NM_023110.3(FGFR1):c.1889T>G (p.Leu630Arg) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"FGFR1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"FGFR1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_023110.3(FGFR1):c.1889T>G (p.Leu630Arg)",
"text": "NM_023110.3(FGFR1):c.1889T>G (p.Leu630Arg) VARIANT_IN_GENE FGFR1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:autosomal_recessive_fgfr1_related_disorders",
"text": "N... | {"gene": "FGFR1", "disease": "Autosomal recessive FGFR1-related disorders", "pathogenic_variants": ["NM_023110.3(FGFR1):c.1889T>G (p.Leu630Arg)"]} | 0.83666 | null |
no_dise_00571 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in NOTCH1 classified as Pathogenic or Likely Pathogenic for Adams-Oliver syndrome 5. | NM_017617.5(NOTCH1):c.3792_3793del (p.Cys1264_Glu1265delinsTer) VARIANT_IN_GENE NOTCH1 → NM_017617.5(NOTCH1):c.3792_3793del (p.Cys1264_Glu1265delinsTer) VARIANT_HAS_CLINICAL_SIGNIFICANCE Adams-Oliver syndrome 5 | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_017617... | NM_017617.5(NOTCH1):c.3792_3793del (p.Cys1264_Glu1265delinsTer) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"NOTCH1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"NOTCH1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_017617.5(NOTCH1):c.3792_3793del (p.Cys1264_Glu1265delinsTer)",
"text": "NM_017617.5(NOTCH1):c.3792_3793del (p.Cys1264_Glu1265delinsTer) VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:adams_oliver_synd... | {"gene": "NOTCH1", "disease": "Adams-Oliver syndrome 5", "pathogenic_variants": ["Single allele", "NM_017617.5(NOTCH1):c.1342del (p.Arg448fs)", "NM_017617.5(NOTCH1):c.1650C>A (p.Tyr550Ter)", "NM_017617.5(NOTCH1):c.3963del (p.Cys1322fs)", "NM_017617.5(NOTCH1):c.5164C>T (p.Gln1722Ter)", "NM_017617.5(NOTCH1):c.2157_2158in... | 0.83666 | null |
no_dise_00192 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRCA2 classified as Pathogenic or Likely Pathogenic for Breast-ovarian cancer, familial, susceptibility to, 2. | NM_000059.4(BRCA2):c.8786del (p.Ala2928_Leu2929insTer) VARIANT_IN_GENE BRCA2 → NM_000059.4(BRCA2):c.8786del (p.Ala2928_Leu2929insTer) VARIANT_HAS_CLINICAL_SIGNIFICANCE Breast-ovarian cancer, familial, susceptibility to, 2 | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA2",
"source_node_type": "GENE",
"source_node_label": "BRCA2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000059.4... | NM_000059.4(BRCA2):c.8786del (p.Ala2928_Leu2929insTer) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRCA2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRCA2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_000059.4(BRCA2):c.8786del (p.Ala2928_Leu2929insTer)",
"text": "NM_000059.4(BRCA2):c.8786del (p.Ala2928_Leu2929insTer) VARIANT_IN_GENE BRCA2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:breast_ovarian_cancer_familial_susce... | {"gene": "BRCA2", "disease": "Breast-ovarian cancer, familial, susceptibility to, 2", "pathogenic_variants": ["NM_000059.4(BRCA2):c.6577G>T (p.Glu2193Ter)", "NM_000059.4(BRCA2):c.4658del (p.Thr1553fs)", "NM_000059.4(BRCA2):c.6065C>A (p.Ser2022Ter)", "NM_000059.4(BRCA2):c.8108_8115delinsTATATAAATAAATAAATAAATATATATTTATTT... | 0.83666 | null |
no_dise_00115 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CHEK2 classified as Pathogenic or Likely Pathogenic for CHEK2-related cancer predisposition. | NM_007194.4(CHEK2):c.1461+1del VARIANT_IN_GENE CHEK2 → NM_007194.4(CHEK2):c.1461+1del VARIANT_HAS_CLINICAL_SIGNIFICANCE CHEK2-related cancer predisposition | {
"steps": [
{
"hop": 1,
"source_node_id": "CHEK2",
"source_node_type": "GENE",
"source_node_label": "CHEK2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007194.4... | NM_007194.4(CHEK2):c.1461+1del | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CHEK2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CHEK2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_007194.4(CHEK2):c.1461+1del",
"text": "NM_007194.4(CHEK2):c.1461+1del VARIANT_IN_GENE CHEK2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:chek2_related_cancer_predisposition",
"text": "NM_007194.4(CHEK2):c.1461+1del VA... | {"gene": "CHEK2", "disease": "CHEK2-related cancer predisposition", "pathogenic_variants": ["NM_007194.4:c.(908+21_909-21)_(1095+21_1096-21)del", "NC_000022.11:g.(?_29092888)_(29095925_?)del", "NC_000022.11:g.(?_29120964)_(29121355_?)del", "NC_000022.11:g.(?_29105993)_(29108005_?)del", "NM_007194.4(CHEK2):c.1241del (p.... | 0.921954 | null |
no_dise_00374 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in DNMT3A classified as Pathogenic or Likely Pathogenic for EBV-positive nodal T- and NK-cell lymphoma. | NM_022552.5(DNMT3A):c.1319G>A (p.Trp440Ter) VARIANT_IN_GENE DNMT3A → NM_022552.5(DNMT3A):c.1319G>A (p.Trp440Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE EBV-positive nodal T- and NK-cell lymphoma | {
"steps": [
{
"hop": 1,
"source_node_id": "DNMT3A",
"source_node_type": "GENE",
"source_node_label": "DNMT3A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_022552... | NM_022552.5(DNMT3A):c.1319G>A (p.Trp440Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"DNMT3A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"DNMT3A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_022552.5(DNMT3A):c.1319G>A (p.Trp440Ter)",
"text": "NM_022552.5(DNMT3A):c.1319G>A (p.Trp440Ter) VARIANT_IN_GENE DNMT3A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:ebv_positive_nodal_t_and_nk_cell_lymphoma",
"text": "... | {"gene": "DNMT3A", "disease": "EBV-positive nodal T- and NK-cell lymphoma", "pathogenic_variants": ["NM_022552.5(DNMT3A):c.1319G>A (p.Trp440Ter)", "NM_022552.5(DNMT3A):c.2250del (p.Phe751fs)", "NM_022552.5(DNMT3A):c.754_760dup (p.Ala254fs)"]} | 0.707107 | null |
no_dise_00163 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in AFP classified as Pathogenic or Likely Pathogenic for Alpha-fetoprotein deficiency. | NM_001134.3(AFP):c.883_884del (p.Leu295fs) VARIANT_IN_GENE AFP → NM_001134.3(AFP):c.883_884del (p.Leu295fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Alpha-fetoprotein deficiency | {
"steps": [
{
"hop": 1,
"source_node_id": "AFP",
"source_node_type": "GENE",
"source_node_label": "AFP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001134.3(AFP... | NM_001134.3(AFP):c.883_884del (p.Leu295fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"AFP\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"AFP\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_001134.3(AFP):c.883_884del (p.Leu295fs)",
"text": "NM_001134.3(AFP):c.883_884del (p.Leu295fs) VARIANT_IN_GENE AFP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:alpha_fetoprotein_deficiency",
"text": "NM_001134.3(AFP):c... | {"gene": "AFP", "disease": "Alpha-fetoprotein deficiency", "pathogenic_variants": ["NM_001134.3(AFP):c.543G>A (p.Trp181Ter)", "NM_001134.3(AFP):c.883_884del (p.Leu295fs)"]} | 0.707107 | null |
no_dise_00410 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in DCTN1 classified as Pathogenic or Likely Pathogenic for DCTN1-related disorder. | NM_004082.5(DCTN1):c.279+1G>T VARIANT_IN_GENE DCTN1 → NM_004082.5(DCTN1):c.279+1G>T VARIANT_HAS_CLINICAL_SIGNIFICANCE DCTN1-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "DCTN1",
"source_node_type": "GENE",
"source_node_label": "DCTN1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004082.5... | NM_004082.5(DCTN1):c.279+1G>T | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"DCTN1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"DCTN1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_004082.5(DCTN1):c.279+1G>T",
"text": "NM_004082.5(DCTN1):c.279+1G>T VARIANT_IN_GENE DCTN1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:dctn1_related_disorder",
"text": "NM_004082.5(DCTN1):c.279+1G>T VARIANT_HAS_CLINIC... | {"gene": "DCTN1", "disease": "DCTN1-related disorder", "pathogenic_variants": ["NM_004082.5(DCTN1):c.279+1G>T"]} | 0.921954 | null |
no_dise_00070 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in VPS35 classified as Pathogenic or Likely Pathogenic for Parkinson disease 17. | NM_018206.6(VPS35):c.2146C>G (p.Gln716Glu) VARIANT_IN_GENE VPS35 → NM_018206.6(VPS35):c.2146C>G (p.Gln716Glu) VARIANT_HAS_CLINICAL_SIGNIFICANCE Parkinson disease 17 | {
"steps": [
{
"hop": 1,
"source_node_id": "VPS35",
"source_node_type": "GENE",
"source_node_label": "VPS35",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_018206.6... | NM_018206.6(VPS35):c.2146C>G (p.Gln716Glu) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"VPS35\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"VPS35\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_018206.6(VPS35):c.2146C>G (p.Gln716Glu)",
"text": "NM_018206.6(VPS35):c.2146C>G (p.Gln716Glu) VARIANT_IN_GENE VPS35",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:parkinson_disease_17",
"text": "NM_018206.6(VPS35):c.214... | {"gene": "VPS35", "disease": "Parkinson disease 17", "pathogenic_variants": ["NM_018206.6(VPS35):c.2146C>G (p.Gln716Glu)"]} | 0.83666 | null |
no_dise_00494 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRCA1 classified as Pathogenic or Likely Pathogenic for Inherited ovarian cancer (without breast cancer). | NM_007294.4(BRCA1):c.5057A>G (p.His1686Arg) VARIANT_IN_GENE BRCA1 → NM_007294.4(BRCA1):c.5057A>G (p.His1686Arg) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inherited ovarian cancer (without breast cancer) | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA1",
"source_node_type": "GENE",
"source_node_label": "BRCA1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007294.4... | NM_007294.4(BRCA1):c.5057A>G (p.His1686Arg) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRCA1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRCA1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_007294.4(BRCA1):c.5057A>G (p.His1686Arg)",
"text": "NM_007294.4(BRCA1):c.5057A>G (p.His1686Arg) VARIANT_IN_GENE BRCA1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inherited_ovarian_cancer_without_breast_cancer",
"text... | {"gene": "BRCA1", "disease": "Inherited ovarian cancer (without breast cancer)", "pathogenic_variants": ["NM_007294.4(BRCA1):c.2850_2851del (p.Arg951fs)", "NM_007294.4(BRCA1):c.135-1G>A", "NM_007294.4(BRCA1):c.5057A>G (p.His1686Arg)"]} | 0.921954 | null |
no_dise_00412 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in ABL1 classified as Pathogenic or Likely Pathogenic for Leukemia, Philadelphia chromosome-positive, resistant to imatinib. | NM_005157.6(ABL1):c.706G>A (p.Glu236Lys) VARIANT_IN_GENE ABL1 → NM_005157.6(ABL1):c.706G>A (p.Glu236Lys) VARIANT_HAS_CLINICAL_SIGNIFICANCE Leukemia, Philadelphia chromosome-positive, resistant to imatinib | {
"steps": [
{
"hop": 1,
"source_node_id": "ABL1",
"source_node_type": "GENE",
"source_node_label": "ABL1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_005157.6(A... | NM_005157.6(ABL1):c.706G>A (p.Glu236Lys) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"ABL1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"ABL1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_005157.6(ABL1):c.706G>A (p.Glu236Lys)",
"text": "NM_005157.6(ABL1):c.706G>A (p.Glu236Lys) VARIANT_IN_GENE ABL1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:leukemia_philadelphia_chromosome_positive_resistant_to_imati",
... | {"gene": "ABL1", "disease": "Leukemia, Philadelphia chromosome-positive, resistant to imatinib", "pathogenic_variants": ["NM_005157.6(ABL1):c.757T>C (p.Tyr253His)", "NM_005157.6(ABL1):c.706G>A (p.Glu236Lys)", "NM_005157.6(ABL1):c.707A>T (p.Glu236Val)"]} | 0.707107 | null |
no_dise_00157 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PDE10A classified as Pathogenic or Likely Pathogenic for Infantile-onset generalized dyskinesia with orofacial involvement. | NM_001385079.1(PDE10A):c.1799T>G (p.Phe600Cys) VARIANT_IN_GENE PDE10A → NM_001385079.1(PDE10A):c.1799T>G (p.Phe600Cys) VARIANT_HAS_CLINICAL_SIGNIFICANCE Infantile-onset generalized dyskinesia with orofacial involvement | {
"steps": [
{
"hop": 1,
"source_node_id": "PDE10A",
"source_node_type": "GENE",
"source_node_label": "PDE10A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001385... | NM_001385079.1(PDE10A):c.1799T>G (p.Phe600Cys) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PDE10A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PDE10A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_001385079.1(PDE10A):c.1799T>G (p.Phe600Cys)",
"text": "NM_001385079.1(PDE10A):c.1799T>G (p.Phe600Cys) VARIANT_IN_GENE PDE10A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:infantile_onset_generalized_dyskinesia_with_orofaci... | {"gene": "PDE10A", "disease": "Infantile-onset generalized dyskinesia with orofacial involvement", "pathogenic_variants": ["NM_001385079.1(PDE10A):c.1799T>G (p.Phe600Cys)", "NM_001385079.1(PDE10A):c.1144G>C (p.Ala382Pro)", "NM_001385079.1(PDE10A):c.686del (p.Gly229fs)", "NM_001385079.1(PDE10A):c.193_200dup (p.Pro68fs)"... | 0.921954 | null |
no_dise_00198 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in DNMT3A classified as Pathogenic or Likely Pathogenic for Hydrocephalus, nonsyndromic, autosomal recessive 2. | GRCh37/hg19 2p23.3(chr2:25437125-25487783)x1 VARIANT_IN_GENE DNMT3A → GRCh37/hg19 2p23.3(chr2:25437125-25487783)x1 VARIANT_HAS_CLINICAL_SIGNIFICANCE Hydrocephalus, nonsyndromic, autosomal recessive 2 | {
"steps": [
{
"hop": 1,
"source_node_id": "DNMT3A",
"source_node_type": "GENE",
"source_node_label": "DNMT3A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "GRCh37/hg... | GRCh37/hg19 2p23.3(chr2:25437125-25487783)x1 | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"DNMT3A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"DNMT3A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "GRCh37/hg19 2p23.3(chr2:25437125-25487783)x1",
"text": "GRCh37/hg19 2p23.3(chr2:25437125-25487783)x1 VARIANT_IN_GENE DNMT3A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hydrocephalus_nonsyndromic_autosomal_recessive_2",
... | {"gene": "DNMT3A", "disease": "Hydrocephalus, nonsyndromic, autosomal recessive 2", "pathogenic_variants": ["GRCh37/hg19 2p23.3(chr2:25437125-25487783)x1"]} | 0.83666 | null |
no_dise_00601 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRCA2 classified as Pathogenic or Likely Pathogenic for Breast-ovarian cancer, familial, susceptibility to, 1. | NM_000059.4(BRCA2):c.2234_2235del (p.Lys745fs) VARIANT_IN_GENE BRCA2 → NM_000059.4(BRCA2):c.2234_2235del (p.Lys745fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Breast-ovarian cancer, familial, susceptibility to, 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA2",
"source_node_type": "GENE",
"source_node_label": "BRCA2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000059.4... | NM_000059.4(BRCA2):c.2234_2235del (p.Lys745fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRCA2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRCA2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_000059.4(BRCA2):c.2234_2235del (p.Lys745fs)",
"text": "NM_000059.4(BRCA2):c.2234_2235del (p.Lys745fs) VARIANT_IN_GENE BRCA2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:breast_ovarian_cancer_familial_susceptibility_to_1",... | {"gene": "BRCA2", "disease": "Breast-ovarian cancer, familial, susceptibility to, 1", "pathogenic_variants": ["NM_000059.4(BRCA2):c.2234_2235del (p.Lys745fs)", "NM_000059.4(BRCA2):c.1094del (p.Pro365fs)", "NM_000059.4(BRCA2):c.4361_4368delinsTCAGAT (p.Pro1454fs)"]} | 0.83666 | null |
no_dise_00018 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in KMT2C classified as Pathogenic or Likely Pathogenic for KMT2C-related disorder. | NM_170606.3(KMT2C):c.14245C>T (p.Pro4749Ser) VARIANT_IN_GENE KMT2C → NM_170606.3(KMT2C):c.14245C>T (p.Pro4749Ser) VARIANT_HAS_CLINICAL_SIGNIFICANCE KMT2C-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2C",
"source_node_type": "GENE",
"source_node_label": "KMT2C",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_170606.3... | NM_170606.3(KMT2C):c.14245C>T (p.Pro4749Ser) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"KMT2C\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"KMT2C\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_170606.3(KMT2C):c.14245C>T (p.Pro4749Ser)",
"text": "NM_170606.3(KMT2C):c.14245C>T (p.Pro4749Ser) VARIANT_IN_GENE KMT2C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:kmt2c_related_disorder",
"text": "NM_170606.3(KMT2C)... | {"gene": "KMT2C", "disease": "KMT2C-related disorder", "pathogenic_variants": ["NM_170606.3(KMT2C):c.8026C>T (p.Gln2676Ter)", "NM_170606.3(KMT2C):c.10449dup (p.Gln3484fs)", "NM_170606.3(KMT2C):c.14245C>T (p.Pro4749Ser)", "NM_170606.3(KMT2C):c.4272del (p.His1424fs)"]} | 0.83666 | null |
no_dise_00384 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRAF classified as Pathogenic or Likely Pathogenic for Paediatric disorders. | NM_004333.6(BRAF):c.1729C>A (p.Leu577Ile) VARIANT_IN_GENE BRAF → NM_004333.6(BRAF):c.1729C>A (p.Leu577Ile) VARIANT_HAS_CLINICAL_SIGNIFICANCE Paediatric disorders | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004333.6(B... | NM_004333.6(BRAF):c.1729C>A (p.Leu577Ile) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRAF\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRAF\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_004333.6(BRAF):c.1729C>A (p.Leu577Ile)",
"text": "NM_004333.6(BRAF):c.1729C>A (p.Leu577Ile) VARIANT_IN_GENE BRAF",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:paediatric_disorders",
"text": "NM_004333.6(BRAF):c.1729C>A... | {"gene": "BRAF", "disease": "Paediatric disorders", "pathogenic_variants": ["NM_004333.6(BRAF):c.1729C>A (p.Leu577Ile)"]} | 0.83666 | null |
no_dise_00278 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in MSH2 classified as Pathogenic or Likely Pathogenic for Uterine corpus cancer. | NM_000251.2(MSH2):c.2459-2_2472del VARIANT_IN_GENE MSH2 → NM_000251.2(MSH2):c.2459-2_2472del VARIANT_HAS_CLINICAL_SIGNIFICANCE Uterine corpus cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH2",
"source_node_type": "GENE",
"source_node_label": "MSH2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000251.2(M... | NM_000251.2(MSH2):c.2459-2_2472del | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"MSH2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"MSH2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_000251.2(MSH2):c.2459-2_2472del",
"text": "NM_000251.2(MSH2):c.2459-2_2472del VARIANT_IN_GENE MSH2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:uterine_corpus_cancer",
"text": "NM_000251.2(MSH2):c.2459-2_2472del VARIA... | {"gene": "MSH2", "disease": "Uterine corpus cancer", "pathogenic_variants": ["NM_000251.2(MSH2):c.2459-2_2472del"]} | 0.707107 | null |
no_dise_00277 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRCA2 classified as Pathogenic or Likely Pathogenic for BRCA2-related cancer predisposition. | NM_000059.4(BRCA2):c.6052del (p.Ser2018fs) VARIANT_IN_GENE BRCA2 → NM_000059.4(BRCA2):c.6052del (p.Ser2018fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE BRCA2-related cancer predisposition | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA2",
"source_node_type": "GENE",
"source_node_label": "BRCA2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000059.4... | NM_000059.4(BRCA2):c.6052del (p.Ser2018fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRCA2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRCA2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_000059.4(BRCA2):c.6052del (p.Ser2018fs)",
"text": "NM_000059.4(BRCA2):c.6052del (p.Ser2018fs) VARIANT_IN_GENE BRCA2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:brca2_related_cancer_predisposition",
"text": "NM_000059... | {"gene": "BRCA2", "disease": "BRCA2-related cancer predisposition", "pathogenic_variants": ["NM_000059.4:c.(1_67+1)del", "NM_000059.4(BRCA2):c.5112_5119delinsG (p.Ile1705fs)", "NM_000059.4(BRCA2):c.8754+1152_9256del", "NM_000059.4(BRCA2):c.8633-6_8635del", "NM_000059.4(BRCA2):c.8469_8478delinsTA (p.Gln2823fs)", "NM_000... | 0.921954 | null |
no_dise_00180 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CHEK2 classified as Pathogenic or Likely Pathogenic for Congenital heart defects, multiple types, 3. | NM_007194.4(CHEK2):c.409C>T (p.Arg137Ter) VARIANT_IN_GENE CHEK2 → NM_007194.4(CHEK2):c.409C>T (p.Arg137Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Congenital heart defects, multiple types, 3 | {
"steps": [
{
"hop": 1,
"source_node_id": "CHEK2",
"source_node_type": "GENE",
"source_node_label": "CHEK2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007194.4... | NM_007194.4(CHEK2):c.409C>T (p.Arg137Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CHEK2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CHEK2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_007194.4(CHEK2):c.409C>T (p.Arg137Ter)",
"text": "NM_007194.4(CHEK2):c.409C>T (p.Arg137Ter) VARIANT_IN_GENE CHEK2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:congenital_heart_defects_multiple_types_3",
"text": "NM_00... | {"gene": "CHEK2", "disease": "Congenital heart defects, multiple types, 3", "pathogenic_variants": ["NM_007194.4(CHEK2):c.409C>T (p.Arg137Ter)"]} | 0.921954 | null |
no_dise_00122 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CBL classified as Pathogenic or Likely Pathogenic for Inborn genetic diseases. | NM_005188.4(CBL):c.1166A>C (p.Lys389Thr) VARIANT_IN_GENE CBL → NM_005188.4(CBL):c.1166A>C (p.Lys389Thr) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inborn genetic diseases | {
"steps": [
{
"hop": 1,
"source_node_id": "CBL",
"source_node_type": "GENE",
"source_node_label": "CBL",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_005188.4(CBL... | NM_005188.4(CBL):c.1166A>C (p.Lys389Thr) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CBL\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CBL\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_005188.4(CBL):c.1166A>C (p.Lys389Thr)",
"text": "NM_005188.4(CBL):c.1166A>C (p.Lys389Thr) VARIANT_IN_GENE CBL",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inborn_genetic_diseases",
"text": "NM_005188.4(CBL):c.1166A>C ... | {"gene": "CBL", "disease": "Inborn genetic diseases", "pathogenic_variants": ["NM_005188.4(CBL):c.1166A>C (p.Lys389Thr)"]} | 0.921954 | null |
no_dise_00593 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in RET classified as Pathogenic or Likely Pathogenic for Medullary thyroid carcinoma. | NM_020975.6(RET):c.2671T>G (p.Ser891Ala) VARIANT_IN_GENE RET → NM_020975.6(RET):c.2671T>G (p.Ser891Ala) VARIANT_HAS_CLINICAL_SIGNIFICANCE Medullary thyroid carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "RET",
"source_node_type": "GENE",
"source_node_label": "RET",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_020975.6(RET... | NM_020975.6(RET):c.2671T>G (p.Ser891Ala) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"RET\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"RET\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_020975.6(RET):c.2671T>G (p.Ser891Ala)",
"text": "NM_020975.6(RET):c.2671T>G (p.Ser891Ala) VARIANT_IN_GENE RET",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:medullary_thyroid_carcinoma",
"text": "NM_020975.6(RET):c.2671... | {"gene": "RET", "disease": "Medullary thyroid carcinoma", "pathogenic_variants": ["NM_020975.6(RET):c.2671T>G (p.Ser891Ala)"]} | 0.921954 | null |
no_dise_00428 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in ANXA11 classified as Pathogenic or Likely Pathogenic for Amyotrophic lateral sclerosis type 23. | NM_145868.2(ANXA11):c.744+1G>A VARIANT_IN_GENE ANXA11 → NM_145868.2(ANXA11):c.744+1G>A VARIANT_HAS_CLINICAL_SIGNIFICANCE Amyotrophic lateral sclerosis type 23 | {
"steps": [
{
"hop": 1,
"source_node_id": "ANXA11",
"source_node_type": "GENE",
"source_node_label": "ANXA11",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_145868... | NM_145868.2(ANXA11):c.744+1G>A | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"ANXA11\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"ANXA11\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_145868.2(ANXA11):c.744+1G>A",
"text": "NM_145868.2(ANXA11):c.744+1G>A VARIANT_IN_GENE ANXA11",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:amyotrophic_lateral_sclerosis_type_23",
"text": "NM_145868.2(ANXA11):c.744+1G>A... | {"gene": "ANXA11", "disease": "Amyotrophic lateral sclerosis type 23", "pathogenic_variants": ["NM_145868.2(ANXA11):c.744+1G>A", "NM_145868.2(ANXA11):c.118G>T (p.Asp40Tyr)", "NM_145868.2(ANXA11):c.112G>A (p.Gly38Arg)", "NM_145868.2(ANXA11):c.119A>G (p.Asp40Gly)"]} | 0.83666 | null |
no_dise_00580 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CREBBP classified as Pathogenic or Likely Pathogenic for Inborn genetic diseases. | NM_004380.3(CREBBP):c.90del (p.Phe30fs) VARIANT_IN_GENE CREBBP → NM_004380.3(CREBBP):c.90del (p.Phe30fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inborn genetic diseases | {
"steps": [
{
"hop": 1,
"source_node_id": "CREBBP",
"source_node_type": "GENE",
"source_node_label": "CREBBP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004380... | NM_004380.3(CREBBP):c.90del (p.Phe30fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CREBBP\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CREBBP\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_004380.3(CREBBP):c.90del (p.Phe30fs)",
"text": "NM_004380.3(CREBBP):c.90del (p.Phe30fs) VARIANT_IN_GENE CREBBP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inborn_genetic_diseases",
"text": "NM_004380.3(CREBBP):c.90de... | {"gene": "CREBBP", "disease": "Inborn genetic diseases", "pathogenic_variants": ["NM_004380.3(CREBBP):c.3G>T (p.Met1Ile)", "NM_004380.3(CREBBP):c.1948T>C (p.Tyr650His)", "NM_004380.3(CREBBP):c.6271A>T (p.Lys2091Ter)", "NM_004380.3(CREBBP):c.4495C>G (p.Leu1499Val)", "NM_004380.3(CREBBP):c.3625C>T (p.Gln1209Ter)", "NM_00... | 0.83666 | null |
no_dise_00594 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in NF1 classified as Pathogenic or Likely Pathogenic for Developmental defect during embryogenesis. | NM_001042492.3(NF1):c.3053_3054insTTCAACTAATTGTTGTTGAAA (p.Leu1018delinsPheSerThrAsnCysCysTer) VARIANT_IN_GENE NF1 → NM_001042492.3(NF1):c.3053_3054insTTCAACTAATTGTTGTTGAAA (p.Leu1018delinsPheSerThrAsnCysCysTer) VARIANT_HAS_CLINICAL_SIGNIFICANCE Developmental defect during embryogenesis | {
"steps": [
{
"hop": 1,
"source_node_id": "NF1",
"source_node_type": "GENE",
"source_node_label": "NF1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001042492.3(... | NM_001042492.3(NF1):c.3053_3054insTTCAACTAATTGTTGTTGAAA (p.Leu1018delinsPheSerThrAsnCysCysTer) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"NF1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"NF1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_001042492.3(NF1):c.3053_3054insTTCAACTAATTGTTGTTGAAA (p.Leu1018delinsPheSerThrAsnCysCysTer)",
"text": "NM_001042492.3(NF1):c.3053_3054insTTCAACTAATTGTTGTTGAAA (p.Leu1018delinsPheSerThrAsnCysCysTer) VARIANT_IN_GENE NF1",
"confidence": 1
},
{
"source_... | {"gene": "NF1", "disease": "Developmental defect during embryogenesis", "pathogenic_variants": ["NM_001042492.3(NF1):c.3053_3054insTTCAACTAATTGTTGTTGAAA (p.Leu1018delinsPheSerThrAsnCysCysTer)"]} | 0.83666 | null |
no_dise_00222 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in TARDBP classified as Pathogenic or Likely Pathogenic for Frontotemporal dementia. | NM_007375.4(TARDBP):c.1129T>C (p.Ser377Pro) VARIANT_IN_GENE TARDBP → NM_007375.4(TARDBP):c.1129T>C (p.Ser377Pro) VARIANT_HAS_CLINICAL_SIGNIFICANCE Frontotemporal dementia | {
"steps": [
{
"hop": 1,
"source_node_id": "TARDBP",
"source_node_type": "GENE",
"source_node_label": "TARDBP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007375... | NM_007375.4(TARDBP):c.1129T>C (p.Ser377Pro) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"TARDBP\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"TARDBP\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_007375.4(TARDBP):c.1129T>C (p.Ser377Pro)",
"text": "NM_007375.4(TARDBP):c.1129T>C (p.Ser377Pro) VARIANT_IN_GENE TARDBP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:frontotemporal_dementia",
"text": "NM_007375.4(TARDBP... | {"gene": "TARDBP", "disease": "Frontotemporal dementia", "pathogenic_variants": ["NM_007375.4(TARDBP):c.1129T>C (p.Ser377Pro)"]} | 0.83666 | null |
no_dise_00463 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRIP1 classified as Pathogenic or Likely Pathogenic for Inherited ovarian cancer (without breast cancer). | NM_032043.3(BRIP1):c.2244C>G (p.Tyr748Ter) VARIANT_IN_GENE BRIP1 → NM_032043.3(BRIP1):c.2244C>G (p.Tyr748Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inherited ovarian cancer (without breast cancer) | {
"steps": [
{
"hop": 1,
"source_node_id": "BRIP1",
"source_node_type": "GENE",
"source_node_label": "BRIP1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_032043.3... | NM_032043.3(BRIP1):c.2244C>G (p.Tyr748Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRIP1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRIP1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_032043.3(BRIP1):c.2244C>G (p.Tyr748Ter)",
"text": "NM_032043.3(BRIP1):c.2244C>G (p.Tyr748Ter) VARIANT_IN_GENE BRIP1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inherited_ovarian_cancer_without_breast_cancer",
"text":... | {"gene": "BRIP1", "disease": "Inherited ovarian cancer (without breast cancer)", "pathogenic_variants": ["NM_032043.3(BRIP1):c.688del (p.Ser230fs)", "NM_032043.3(BRIP1):c.1888dup (p.Thr630fs)", "NM_032043.3(BRIP1):c.2244C>G (p.Tyr748Ter)", "NM_032043.3(BRIP1):c.1495C>T (p.Gln499Ter)", "NM_032043.3(BRIP1):c.918+1G>A", "... | 0.921954 | null |
no_dise_00394 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in KDM6A classified as Pathogenic or Likely Pathogenic for Kabuki syndrome 1. | NM_001291415.2(KDM6A):c.133dup (p.Glu45fs) VARIANT_IN_GENE KDM6A → NM_001291415.2(KDM6A):c.133dup (p.Glu45fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Kabuki syndrome 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "KDM6A",
"source_node_type": "GENE",
"source_node_label": "KDM6A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_00129141... | NM_001291415.2(KDM6A):c.133dup (p.Glu45fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"KDM6A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"KDM6A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_001291415.2(KDM6A):c.133dup (p.Glu45fs)",
"text": "NM_001291415.2(KDM6A):c.133dup (p.Glu45fs) VARIANT_IN_GENE KDM6A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:kabuki_syndrome_1",
"text": "NM_001291415.2(KDM6A):c.133... | {"gene": "KDM6A", "disease": "Kabuki syndrome 1", "pathogenic_variants": ["NM_001291415.2(KDM6A):c.133dup (p.Glu45fs)"]} | 0.83666 | null |
no_dise_00488 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BCHE classified as Pathogenic or Likely Pathogenic for BCHE Newfoundland. | BCHE Newfoundland VARIANT_IN_GENE BCHE → BCHE Newfoundland VARIANT_HAS_CLINICAL_SIGNIFICANCE BCHE Newfoundland | {
"steps": [
{
"hop": 1,
"source_node_id": "BCHE",
"source_node_type": "GENE",
"source_node_label": "BCHE",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "BCHE Newfound... | BCHE Newfoundland | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BCHE\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BCHE\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "BCHE Newfoundland",
"text": "BCHE Newfoundland VARIANT_IN_GENE BCHE",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:bche_newfoundland",
"text": "BCHE Newfoundland VARIANT_HAS_CLINICAL_SIGNIFICANCE BCHE Newfoundland",
"c... | {"gene": "BCHE", "disease": "BCHE Newfoundland", "pathogenic_variants": ["BCHE Newfoundland"]} | 0.707107 | null |
no_dise_00466 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in TARDBP classified as Pathogenic or Likely Pathogenic for FRONTOTEMPORAL DEMENTIA WITH TDP43 INCLUSIONS, TARDBP-RELATED. | NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu) VARIANT_IN_GENE TARDBP → NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu) VARIANT_HAS_CLINICAL_SIGNIFICANCE FRONTOTEMPORAL DEMENTIA WITH TDP43 INCLUSIONS, TARDBP-RELATED | {
"steps": [
{
"hop": 1,
"source_node_id": "TARDBP",
"source_node_type": "GENE",
"source_node_label": "TARDBP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007375... | NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"TARDBP\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"TARDBP\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu)",
"text": "NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu) VARIANT_IN_GENE TARDBP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:frontotemporal_dementia_with_tdp43_inclusions_tardbp_relate... | {"gene": "TARDBP", "disease": "FRONTOTEMPORAL DEMENTIA WITH TDP43 INCLUSIONS, TARDBP-RELATED", "pathogenic_variants": ["NM_007375.4(TARDBP):c.787A>G (p.Lys263Glu)"]} | 0.707107 | null |
no_dise_00584 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRAF classified as Pathogenic or Likely Pathogenic for LEOPARD syndrome 3. | NM_004333.6(BRAF):c.1801A>C (p.Lys601Gln) VARIANT_IN_GENE BRAF → NM_004333.6(BRAF):c.1801A>C (p.Lys601Gln) VARIANT_HAS_CLINICAL_SIGNIFICANCE LEOPARD syndrome 3 | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004333.6(B... | NM_004333.6(BRAF):c.1801A>C (p.Lys601Gln) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRAF\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRAF\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_004333.6(BRAF):c.1801A>C (p.Lys601Gln)",
"text": "NM_004333.6(BRAF):c.1801A>C (p.Lys601Gln) VARIANT_IN_GENE BRAF",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:leopard_syndrome_3",
"text": "NM_004333.6(BRAF):c.1801A>C (... | {"gene": "BRAF", "disease": "LEOPARD syndrome 3", "pathogenic_variants": ["NM_004333.6(BRAF):c.1801A>C (p.Lys601Gln)", "NM_004333.6(BRAF):c.1802A>T (p.Lys601Ile)"]} | 0.921954 | null |
no_dise_00592 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CDH1 classified as Pathogenic or Likely Pathogenic for Malignant tumor of breast. | NC_000016.9:g.(68771367_68772199)_(68772315_68835572)del VARIANT_IN_GENE CDH1 → NC_000016.9:g.(68771367_68772199)_(68772315_68835572)del VARIANT_HAS_CLINICAL_SIGNIFICANCE Malignant tumor of breast | {
"steps": [
{
"hop": 1,
"source_node_id": "CDH1",
"source_node_type": "GENE",
"source_node_label": "CDH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NC_000016.9:g... | NC_000016.9:g.(68771367_68772199)_(68772315_68835572)del | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CDH1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CDH1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NC_000016.9:g.(68771367_68772199)_(68772315_68835572)del",
"text": "NC_000016.9:g.(68771367_68772199)_(68772315_68835572)del VARIANT_IN_GENE CDH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:malignant_tumor_of_breast",
"... | {"gene": "CDH1", "disease": "Malignant tumor of breast", "pathogenic_variants": ["NC_000016.9:g.(68771367_68772199)_(68772315_68835572)del", "NM_004360.5(CDH1):c.2440-2_*1del", "NC_000016.9:g.(68857530_68862076)_(68863701_68867192)dup"]} | 0.83666 | null |
no_dise_00485 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CTNNA1 classified as Pathogenic or Likely Pathogenic for Craniosynostosis syndrome. | NM_001903.5(CTNNA1):c.2572_2586dup (p.Ser858_Lys862dup) VARIANT_IN_GENE CTNNA1 → NM_001903.5(CTNNA1):c.2572_2586dup (p.Ser858_Lys862dup) VARIANT_HAS_CLINICAL_SIGNIFICANCE Craniosynostosis syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "CTNNA1",
"source_node_type": "GENE",
"source_node_label": "CTNNA1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001903... | NM_001903.5(CTNNA1):c.2572_2586dup (p.Ser858_Lys862dup) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CTNNA1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CTNNA1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_001903.5(CTNNA1):c.2572_2586dup (p.Ser858_Lys862dup)",
"text": "NM_001903.5(CTNNA1):c.2572_2586dup (p.Ser858_Lys862dup) VARIANT_IN_GENE CTNNA1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:craniosynostosis_syndrome",
"... | {"gene": "CTNNA1", "disease": "Craniosynostosis syndrome", "pathogenic_variants": ["NM_001903.5(CTNNA1):c.2572_2586dup (p.Ser858_Lys862dup)"]} | 0.707107 | null |
no_dise_00272 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in RAD51D classified as Pathogenic or Likely Pathogenic for Familial ovarian cancer. | NM_002878.4(RAD51D):c.536dup (p.Asp180fs) VARIANT_IN_GENE RAD51D → NM_002878.4(RAD51D):c.536dup (p.Asp180fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Familial ovarian cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "RAD51D",
"source_node_type": "GENE",
"source_node_label": "RAD51D",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_002878... | NM_002878.4(RAD51D):c.536dup (p.Asp180fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"RAD51D\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"RAD51D\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_002878.4(RAD51D):c.536dup (p.Asp180fs)",
"text": "NM_002878.4(RAD51D):c.536dup (p.Asp180fs) VARIANT_IN_GENE RAD51D",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:familial_ovarian_cancer",
"text": "NM_002878.4(RAD51D):c.... | {"gene": "RAD51D", "disease": "Familial ovarian cancer", "pathogenic_variants": ["NM_002878.4(RAD51D):c.547C>T (p.Gln183Ter)", "NM_002878.4(RAD51D):c.748del (p.His250fs)", "NM_002878.4(RAD51D):c.536dup (p.Asp180fs)", "NM_002878.4(RAD51D):c.144+1G>A"]} | 0.83666 | null |
no_dise_00006 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PMS2 classified as Pathogenic or Likely Pathogenic for PMS2-related disorder. | NM_000535.7(PMS2):c.1438G>T (p.Gly480Ter) VARIANT_IN_GENE PMS2 → NM_000535.7(PMS2):c.1438G>T (p.Gly480Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE PMS2-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000535.7(P... | NM_000535.7(PMS2):c.1438G>T (p.Gly480Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PMS2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PMS2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_000535.7(PMS2):c.1438G>T (p.Gly480Ter)",
"text": "NM_000535.7(PMS2):c.1438G>T (p.Gly480Ter) VARIANT_IN_GENE PMS2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:pms2_related_disorder",
"text": "NM_000535.7(PMS2):c.1438G>... | {"gene": "PMS2", "disease": "PMS2-related disorder", "pathogenic_variants": ["NM_000535.7(PMS2):c.1438G>T (p.Gly480Ter)"]} | 0.707107 | null |
no_dise_00343 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in RET classified as Pathogenic or Likely Pathogenic for Abnormality of the digestive system. | NM_020975.6(RET):c.960del (p.Asp322fs) VARIANT_IN_GENE RET → NM_020975.6(RET):c.960del (p.Asp322fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Abnormality of the digestive system | {
"steps": [
{
"hop": 1,
"source_node_id": "RET",
"source_node_type": "GENE",
"source_node_label": "RET",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_020975.6(RET... | NM_020975.6(RET):c.960del (p.Asp322fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"RET\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"RET\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_020975.6(RET):c.960del (p.Asp322fs)",
"text": "NM_020975.6(RET):c.960del (p.Asp322fs) VARIANT_IN_GENE RET",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:abnormality_of_the_digestive_system",
"text": "NM_020975.6(RET):c.... | {"gene": "RET", "disease": "Abnormality of the digestive system", "pathogenic_variants": ["NM_020975.6(RET):c.960del (p.Asp322fs)"]} | 0.83666 | null |
no_dise_00368 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in RAD51D classified as Pathogenic or Likely Pathogenic for Deleterious RAD51D Gene Mutation. | NM_002878.4(RAD51D):c.620C>A (p.Ser207Ter) VARIANT_IN_GENE RAD51D → NM_002878.4(RAD51D):c.620C>A (p.Ser207Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Deleterious RAD51D Gene Mutation | {
"steps": [
{
"hop": 1,
"source_node_id": "RAD51D",
"source_node_type": "GENE",
"source_node_label": "RAD51D",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_002878... | NM_002878.4(RAD51D):c.620C>A (p.Ser207Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"RAD51D\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"RAD51D\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_002878.4(RAD51D):c.620C>A (p.Ser207Ter)",
"text": "NM_002878.4(RAD51D):c.620C>A (p.Ser207Ter) VARIANT_IN_GENE RAD51D",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:deleterious_rad51d_gene_mutation",
"text": "NM_002878.4... | {"gene": "RAD51D", "disease": "Deleterious RAD51D Gene Mutation", "pathogenic_variants": ["NM_002878.4(RAD51D):c.564_567del (p.Val189fs)", "NM_002878.4(RAD51D):c.620C>A (p.Ser207Ter)"]} | 0.83666 | null |
no_dise_00226 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PFN1 classified as Pathogenic or Likely Pathogenic for PAGET DISEASE OF BONE 7, EARLY-ONSET. | PFN1, 4-BP DEL, 318TGAC VARIANT_IN_GENE PFN1 → PFN1, 4-BP DEL, 318TGAC VARIANT_HAS_CLINICAL_SIGNIFICANCE PAGET DISEASE OF BONE 7, EARLY-ONSET | {
"steps": [
{
"hop": 1,
"source_node_id": "PFN1",
"source_node_type": "GENE",
"source_node_label": "PFN1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "PFN1, 4-BP DE... | PFN1, 4-BP DEL, 318TGAC | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PFN1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PFN1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "PFN1, 4-BP DEL, 318TGAC",
"text": "PFN1, 4-BP DEL, 318TGAC VARIANT_IN_GENE PFN1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:paget_disease_of_bone_7_early_onset",
"text": "PFN1, 4-BP DEL, 318TGAC VARIANT_HAS_CLINICAL_SIG... | {"gene": "PFN1", "disease": "PAGET DISEASE OF BONE 7, EARLY-ONSET", "pathogenic_variants": ["NM_005022.4(PFN1):c.325+10T>C", "PFN1, 1-BP DEL, 324G", "PFN1, 4-BP DEL, 318TGAC"]} | 0.707107 | null |
no_dise_00242 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in POLD1 classified as Pathogenic or Likely Pathogenic for Immunodeficiency 120. | NM_002691.4(POLD1):c.[2052G>C;2816C>G] VARIANT_IN_GENE POLD1 → NM_002691.4(POLD1):c.[2052G>C;2816C>G] VARIANT_HAS_CLINICAL_SIGNIFICANCE Immunodeficiency 120 | {
"steps": [
{
"hop": 1,
"source_node_id": "POLD1",
"source_node_type": "GENE",
"source_node_label": "POLD1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_002691.4... | NM_002691.4(POLD1):c.[2052G>C;2816C>G] | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"POLD1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"POLD1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_002691.4(POLD1):c.2052G>C (p.Gln684His)",
"text": "NM_002691.4(POLD1):c.[2052G>C;2816C>G] VARIANT_IN_GENE POLD1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:immunodeficiency_120",
"text": "NM_002691.4(POLD1):c.[2052G>... | {"gene": "POLD1", "disease": "Immunodeficiency 120", "pathogenic_variants": ["NM_002691.4(POLD1):c.[2052G>C;2816C>G]"]} | 0.707107 | null |
no_dise_00610 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in NLRP3 classified as Pathogenic or Likely Pathogenic for Pericardial effusion. | NM_001243133.2(NLRP3):c.1799A>G (p.Gln600Arg) VARIANT_IN_GENE NLRP3 → NM_001243133.2(NLRP3):c.1799A>G (p.Gln600Arg) VARIANT_HAS_CLINICAL_SIGNIFICANCE Pericardial effusion | {
"steps": [
{
"hop": 1,
"source_node_id": "NLRP3",
"source_node_type": "GENE",
"source_node_label": "NLRP3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_00124313... | NM_001243133.2(NLRP3):c.1799A>G (p.Gln600Arg) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"NLRP3\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"NLRP3\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_001243133.2(NLRP3):c.1799A>G (p.Gln600Arg)",
"text": "NM_001243133.2(NLRP3):c.1799A>G (p.Gln600Arg) VARIANT_IN_GENE NLRP3",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:pericardial_effusion",
"text": "NM_001243133.2(NLR... | {"gene": "NLRP3", "disease": "Pericardial effusion", "pathogenic_variants": ["NM_001243133.2(NLRP3):c.1799A>G (p.Gln600Arg)"]} | 0.707107 | null |
no_dise_00276 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in NF1 classified as Pathogenic or Likely Pathogenic for Neurofibromatosis-Noonan syndrome. | NM_001042492.3(NF1):c.6452_6453del (p.Leu2151fs) VARIANT_IN_GENE NF1 → NM_001042492.3(NF1):c.6452_6453del (p.Leu2151fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Neurofibromatosis-Noonan syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "NF1",
"source_node_type": "GENE",
"source_node_label": "NF1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001042492.3(... | NM_001042492.3(NF1):c.6452_6453del (p.Leu2151fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"NF1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"NF1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_001042492.3(NF1):c.6452_6453del (p.Leu2151fs)",
"text": "NM_001042492.3(NF1):c.6452_6453del (p.Leu2151fs) VARIANT_IN_GENE NF1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:neurofibromatosis_noonan_syndrome",
"text": "N... | {"gene": "NF1", "disease": "Neurofibromatosis-Noonan syndrome", "pathogenic_variants": ["NM_001042492.3(NF1):c.6452_6453del (p.Leu2151fs)"]} | 0.83666 | null |
no_dise_00105 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BCL11B classified as Pathogenic or Likely Pathogenic for Combined immunodeficiency. | NM_138576.4(BCL11B):c.1323T>G (p.Asn441Lys) VARIANT_IN_GENE BCL11B → NM_138576.4(BCL11B):c.1323T>G (p.Asn441Lys) VARIANT_HAS_CLINICAL_SIGNIFICANCE Combined immunodeficiency | {
"steps": [
{
"hop": 1,
"source_node_id": "BCL11B",
"source_node_type": "GENE",
"source_node_label": "BCL11B",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_138576... | NM_138576.4(BCL11B):c.1323T>G (p.Asn441Lys) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BCL11B\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BCL11B\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_138576.4(BCL11B):c.1323T>G (p.Asn441Lys)",
"text": "NM_138576.4(BCL11B):c.1323T>G (p.Asn441Lys) VARIANT_IN_GENE BCL11B",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:combined_immunodeficiency",
"text": "NM_138576.4(BCL1... | {"gene": "BCL11B", "disease": "Combined immunodeficiency", "pathogenic_variants": ["NM_138576.4(BCL11B):c.1323T>G (p.Asn441Lys)"]} | 0.707107 | null |
no_dise_00285 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in APC classified as Pathogenic or Likely Pathogenic for Inherited polyposis and early onset colorectal cancer - germline testing. | NM_000038.6(APC):c.4175C>G (p.Ser1392Ter) VARIANT_IN_GENE APC → NM_000038.6(APC):c.4175C>G (p.Ser1392Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inherited polyposis and early onset colorectal cancer - germline testing | {
"steps": [
{
"hop": 1,
"source_node_id": "APC",
"source_node_type": "GENE",
"source_node_label": "APC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000038.6(APC... | NM_000038.6(APC):c.4175C>G (p.Ser1392Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"APC\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"APC\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_000038.6(APC):c.4175C>G (p.Ser1392Ter)",
"text": "NM_000038.6(APC):c.4175C>G (p.Ser1392Ter) VARIANT_IN_GENE APC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inherited_polyposis_and_early_onset_colorectal_cancer_germli",
... | {"gene": "APC", "disease": "Inherited polyposis and early onset colorectal cancer - germline testing", "pathogenic_variants": ["NM_000038.6(APC):c.4175C>G (p.Ser1392Ter)"]} | 0.83666 | null |
no_dise_00066 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in DDX41 classified as Pathogenic or Likely Pathogenic for DDX41-related hematologic malignancy predisposition syndrome. | NM_016222.4(DDX41):c.1586_1587del (p.Thr529fs) VARIANT_IN_GENE DDX41 → NM_016222.4(DDX41):c.1586_1587del (p.Thr529fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE DDX41-related hematologic malignancy predisposition syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "DDX41",
"source_node_type": "GENE",
"source_node_label": "DDX41",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_016222.4... | NM_016222.4(DDX41):c.1586_1587del (p.Thr529fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"DDX41\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"DDX41\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_016222.4(DDX41):c.1586_1587del (p.Thr529fs)",
"text": "NM_016222.4(DDX41):c.1586_1587del (p.Thr529fs) VARIANT_IN_GENE DDX41",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:ddx41_related_hematologic_malignancy_predisposition_... | {"gene": "DDX41", "disease": "DDX41-related hematologic malignancy predisposition syndrome", "pathogenic_variants": ["NM_016222.4(DDX41):c.1301del (p.Pro434fs)", "NM_016222.4(DDX41):c.2T>C (p.Met1Thr)", "NM_016222.4(DDX41):c.1621_1621+10del", "NM_016222.4(DDX41):c.547T>A (p.Phe183Ile)", "NM_016222.4(DDX41):c.434+1G>T",... | 0.921954 | null |
no_dise_00324 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in DCTN1 classified as Pathogenic or Likely Pathogenic for Perry syndrome. | NM_004082.5(DCTN1):c.279+1G>C VARIANT_IN_GENE DCTN1 → NM_004082.5(DCTN1):c.279+1G>C VARIANT_HAS_CLINICAL_SIGNIFICANCE Perry syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "DCTN1",
"source_node_type": "GENE",
"source_node_label": "DCTN1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004082.5... | NM_004082.5(DCTN1):c.279+1G>C | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"DCTN1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"DCTN1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_004082.5(DCTN1):c.279+1G>C",
"text": "NM_004082.5(DCTN1):c.279+1G>C VARIANT_IN_GENE DCTN1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:perry_syndrome",
"text": "NM_004082.5(DCTN1):c.279+1G>C VARIANT_HAS_CLINICAL_SIGNI... | {"gene": "DCTN1", "disease": "Perry syndrome", "pathogenic_variants": ["NM_004082.5(DCTN1):c.626dup (p.Leu210fs)", "NM_004082.5(DCTN1):c.279+1G>C"]} | 0.921954 | null |
no_dise_00387 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in KIF5A classified as Pathogenic or Likely Pathogenic for Spastic Paraglegia 10. | NM_004984.4(KIF5A):c.1550_1554del (p.Asp517fs) VARIANT_IN_GENE KIF5A → NM_004984.4(KIF5A):c.1550_1554del (p.Asp517fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Spastic Paraglegia 10 | {
"steps": [
{
"hop": 1,
"source_node_id": "KIF5A",
"source_node_type": "GENE",
"source_node_label": "KIF5A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004984.4... | NM_004984.4(KIF5A):c.1550_1554del (p.Asp517fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"KIF5A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"KIF5A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_004984.4(KIF5A):c.1550_1554del (p.Asp517fs)",
"text": "NM_004984.4(KIF5A):c.1550_1554del (p.Asp517fs) VARIANT_IN_GENE KIF5A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:spastic_paraglegia_10",
"text": "NM_004984.4(KIF... | {"gene": "KIF5A", "disease": "Spastic Paraglegia 10", "pathogenic_variants": ["NM_004984.4(KIF5A):c.1550_1554del (p.Asp517fs)", "NM_004984.4(KIF5A):c.404_407del (p.Tyr135fs)", "NM_004984.4(KIF5A):c.2549_2562dup (p.Arg855fs)"]} | 0.83666 | null |
no_dise_00398 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in KIF5A classified as Pathogenic or Likely Pathogenic for Hereditary spastic paraplegia. | NM_004984.4(KIF5A):c.868G>C (p.Asp290His) VARIANT_IN_GENE KIF5A → NM_004984.4(KIF5A):c.868G>C (p.Asp290His) VARIANT_HAS_CLINICAL_SIGNIFICANCE Hereditary spastic paraplegia | {
"steps": [
{
"hop": 1,
"source_node_id": "KIF5A",
"source_node_type": "GENE",
"source_node_label": "KIF5A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004984.4... | NM_004984.4(KIF5A):c.868G>C (p.Asp290His) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"KIF5A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"KIF5A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_004984.4(KIF5A):c.868G>C (p.Asp290His)",
"text": "NM_004984.4(KIF5A):c.868G>C (p.Asp290His) VARIANT_IN_GENE KIF5A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hereditary_spastic_paraplegia",
"text": "NM_004984.4(KIF5A... | {"gene": "KIF5A", "disease": "Hereditary spastic paraplegia", "pathogenic_variants": ["NM_004984.4(KIF5A):c.868G>C (p.Asp290His)"]} | 0.83666 | null |
no_dise_00235 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in RET classified as Pathogenic or Likely Pathogenic for Multiple endocrine neoplasia, type 2. | NM_020975.6(RET):c.1522+2T>C VARIANT_IN_GENE RET → NM_020975.6(RET):c.1522+2T>C VARIANT_HAS_CLINICAL_SIGNIFICANCE Multiple endocrine neoplasia, type 2 | {
"steps": [
{
"hop": 1,
"source_node_id": "RET",
"source_node_type": "GENE",
"source_node_label": "RET",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_020975.6(RET... | NM_020975.6(RET):c.1522+2T>C | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"RET\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"RET\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_020975.6(RET):c.1522+2T>C",
"text": "NM_020975.6(RET):c.1522+2T>C VARIANT_IN_GENE RET",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:multiple_endocrine_neoplasia_type_2",
"text": "NM_020975.6(RET):c.1522+2T>C VARIANT_HA... | {"gene": "RET", "disease": "Multiple endocrine neoplasia, type 2", "pathogenic_variants": ["NM_020975.6(RET):c.206del (p.Gly69fs)", "NM_020975.6(RET):c.1341del (p.Asn448fs)", "NM_020975.6(RET):c.758dup (p.Val254fs)", "NM_020975.6(RET):c.2715C>A (p.Tyr905Ter)", "NM_020975.6(RET):c.668_669dup (p.Ser224Ter)", "NM_020975.6... | 0.83666 | null |
no_dise_00332 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in MET classified as Pathogenic or Likely Pathogenic for Papillary renal cell carcinoma type 1. | NM_000245.4(MET):c.3562G>T (p.Val1188Leu) VARIANT_IN_GENE MET → NM_000245.4(MET):c.3562G>T (p.Val1188Leu) VARIANT_HAS_CLINICAL_SIGNIFICANCE Papillary renal cell carcinoma type 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "MET",
"source_node_type": "GENE",
"source_node_label": "MET",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000245.4(MET... | NM_000245.4(MET):c.3562G>T (p.Val1188Leu) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"MET\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"MET\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_000245.4(MET):c.3562G>T (p.Val1188Leu)",
"text": "NM_000245.4(MET):c.3562G>T (p.Val1188Leu) VARIANT_IN_GENE MET",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:papillary_renal_cell_carcinoma_type_1",
"text": "NM_000245.4... | {"gene": "MET", "disease": "Papillary renal cell carcinoma type 1", "pathogenic_variants": ["NM_000245.4(MET):c.3562G>T (p.Val1188Leu)"]} | 0.707107 | null |
no_dise_00478 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PFN1 classified as Pathogenic or Likely Pathogenic for Amyotrophic lateral sclerosis type 18. | NM_005022.4(PFN1):c.318_319dup (p.Asp107fs) VARIANT_IN_GENE PFN1 → NM_005022.4(PFN1):c.318_319dup (p.Asp107fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Amyotrophic lateral sclerosis type 18 | {
"steps": [
{
"hop": 1,
"source_node_id": "PFN1",
"source_node_type": "GENE",
"source_node_label": "PFN1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_005022.4(P... | NM_005022.4(PFN1):c.318_319dup (p.Asp107fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PFN1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PFN1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_005022.4(PFN1):c.318_319dup (p.Asp107fs)",
"text": "NM_005022.4(PFN1):c.318_319dup (p.Asp107fs) VARIANT_IN_GENE PFN1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:amyotrophic_lateral_sclerosis_type_18",
"text": "NM_005... | {"gene": "PFN1", "disease": "Amyotrophic lateral sclerosis type 18", "pathogenic_variants": ["NM_005022.4(PFN1):c.318_319dup (p.Asp107fs)"]} | 0.921954 | null |
no_dise_00301 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in ERG classified as Pathogenic or Likely Pathogenic for Neurofibromatosis, type 1. | t(21;22)(q21;q12) VARIANT_IN_GENE ERG → t(21;22)(q21;q12) VARIANT_HAS_CLINICAL_SIGNIFICANCE Neurofibromatosis, type 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "ERG",
"source_node_type": "GENE",
"source_node_label": "ERG",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "t(21;22)(q21;q1... | t(21;22)(q21;q12) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"ERG\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"ERG\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "t(21;22)(q21;q12)",
"text": "t(21;22)(q21;q12) VARIANT_IN_GENE ERG",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:neurofibromatosis_type_1",
"text": "t(21;22)(q21;q12) VARIANT_HAS_CLINICAL_SIGNIFICANCE Neurofibromatosis, t... | {"gene": "ERG", "disease": "Neurofibromatosis, type 1", "pathogenic_variants": ["t(21;22)(q21;q12)"]} | 0.707107 | null |
no_dise_00089 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CBL classified as Pathogenic or Likely Pathogenic for Cardiovascular phenotype. | NM_005188.4(CBL):c.1109_1111dup (p.Leu370_Tyr371insLeu) VARIANT_IN_GENE CBL → NM_005188.4(CBL):c.1109_1111dup (p.Leu370_Tyr371insLeu) VARIANT_HAS_CLINICAL_SIGNIFICANCE Cardiovascular phenotype | {
"steps": [
{
"hop": 1,
"source_node_id": "CBL",
"source_node_type": "GENE",
"source_node_label": "CBL",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_005188.4(CBL... | NM_005188.4(CBL):c.1109_1111dup (p.Leu370_Tyr371insLeu) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CBL\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CBL\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_005188.4(CBL):c.1109_1111dup (p.Leu370_Tyr371insLeu)",
"text": "NM_005188.4(CBL):c.1109_1111dup (p.Leu370_Tyr371insLeu) VARIANT_IN_GENE CBL",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:cardiovascular_phenotype",
"text... | {"gene": "CBL", "disease": "Cardiovascular phenotype", "pathogenic_variants": ["NM_005188.4(CBL):c.1109_1111dup (p.Leu370_Tyr371insLeu)"]} | 0.83666 | null |
no_dise_00554 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BIN1 classified as Pathogenic or Likely Pathogenic for Myopathy, centronuclear, 2. | NM_139343.3(BIN1):c.105G>T (p.Lys35Asn) VARIANT_IN_GENE BIN1 → NM_139343.3(BIN1):c.105G>T (p.Lys35Asn) VARIANT_HAS_CLINICAL_SIGNIFICANCE Myopathy, centronuclear, 2 | {
"steps": [
{
"hop": 1,
"source_node_id": "BIN1",
"source_node_type": "GENE",
"source_node_label": "BIN1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_139343.3(B... | NM_139343.3(BIN1):c.105G>T (p.Lys35Asn) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BIN1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BIN1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_139343.3(BIN1):c.105G>T (p.Lys35Asn)",
"text": "NM_139343.3(BIN1):c.105G>T (p.Lys35Asn) VARIANT_IN_GENE BIN1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:myopathy_centronuclear_2",
"text": "NM_139343.3(BIN1):c.105G>T ... | {"gene": "BIN1", "disease": "Myopathy, centronuclear, 2", "pathogenic_variants": ["NM_139343.3(BIN1):c.1713G>A (p.Trp571Ter)", "NM_139343.3(BIN1):c.451G>A (p.Asp151Asn)", "NM_139343.3(BIN1):c.105G>T (p.Lys35Asn)", "NM_139343.3(BIN1):c.166-2_220+3del", "NM_139343.3(BIN1):c.433C>T (p.Arg145Cys)", "NM_139343.3(BIN1):c.172... | 0.707107 | null |
no_dise_00087 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in REST classified as Pathogenic or Likely Pathogenic for Autosomal dominant nonsyndromic hearing loss 27. | NM_005612.5(REST):c.983-2247C>G VARIANT_IN_GENE REST → NM_005612.5(REST):c.983-2247C>G VARIANT_HAS_CLINICAL_SIGNIFICANCE Autosomal dominant nonsyndromic hearing loss 27 | {
"steps": [
{
"hop": 1,
"source_node_id": "REST",
"source_node_type": "GENE",
"source_node_label": "REST",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_005612.5(R... | NM_005612.5(REST):c.983-2247C>G | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"REST\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"REST\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_005612.5(REST):c.983-2247C>G",
"text": "NM_005612.5(REST):c.983-2247C>G VARIANT_IN_GENE REST",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:autosomal_dominant_nonsyndromic_hearing_loss_27",
"text": "NM_005612.5(REST):c.... | {"gene": "REST", "disease": "Autosomal dominant nonsyndromic hearing loss 27", "pathogenic_variants": ["NM_005612.5(REST):c.983-2247C>G"]} | 0.707107 | null |
no_dise_00450 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PSEN1 classified as Pathogenic or Likely Pathogenic for Early-onset autosomal dominant Alzheimer disease. | NM_000021.4(PSEN1):c.856C>G (p.Leu286Val) VARIANT_IN_GENE PSEN1 → NM_000021.4(PSEN1):c.856C>G (p.Leu286Val) VARIANT_HAS_CLINICAL_SIGNIFICANCE Early-onset autosomal dominant Alzheimer disease | {
"steps": [
{
"hop": 1,
"source_node_id": "PSEN1",
"source_node_type": "GENE",
"source_node_label": "PSEN1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000021.4... | NM_000021.4(PSEN1):c.856C>G (p.Leu286Val) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PSEN1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PSEN1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_000021.4(PSEN1):c.856C>G (p.Leu286Val)",
"text": "NM_000021.4(PSEN1):c.856C>G (p.Leu286Val) VARIANT_IN_GENE PSEN1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:early_onset_autosomal_dominant_alzheimer_disease",
"text":... | {"gene": "PSEN1", "disease": "Early-onset autosomal dominant Alzheimer disease", "pathogenic_variants": ["NM_000021.4(PSEN1):c.856C>G (p.Leu286Val)", "NM_000021.4(PSEN1):c.498TAT[1] (p.Ile168del)"]} | 0.921954 | null |
no_dise_00541 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in KMT2D classified as Pathogenic or Likely Pathogenic for Neurodevelopmental abnormality. | NM_003482.4(KMT2D):c.7762del (p.His2588fs) VARIANT_IN_GENE KMT2D → NM_003482.4(KMT2D):c.7762del (p.His2588fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Neurodevelopmental abnormality | {
"steps": [
{
"hop": 1,
"source_node_id": "KMT2D",
"source_node_type": "GENE",
"source_node_label": "KMT2D",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_003482.4... | NM_003482.4(KMT2D):c.7762del (p.His2588fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"KMT2D\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"KMT2D\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_003482.4(KMT2D):c.7762del (p.His2588fs)",
"text": "NM_003482.4(KMT2D):c.7762del (p.His2588fs) VARIANT_IN_GENE KMT2D",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:neurodevelopmental_abnormality",
"text": "NM_003482.4(KM... | {"gene": "KMT2D", "disease": "Neurodevelopmental abnormality", "pathogenic_variants": ["NM_003482.4(KMT2D):c.7762del (p.His2588fs)"]} | 0.83666 | null |
no_dise_00026 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in MSH6 classified as Pathogenic or Likely Pathogenic for Breast and/or ovarian cancer. | NM_000179.3(MSH6):c.3917_3938dup (p.Ile1313_Gln1314insTer) VARIANT_IN_GENE MSH6 → NM_000179.3(MSH6):c.3917_3938dup (p.Ile1313_Gln1314insTer) VARIANT_HAS_CLINICAL_SIGNIFICANCE Breast and/or ovarian cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH6",
"source_node_type": "GENE",
"source_node_label": "MSH6",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000179.3(M... | NM_000179.3(MSH6):c.3917_3938dup (p.Ile1313_Gln1314insTer) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"MSH6\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"MSH6\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_000179.3(MSH6):c.3917_3938dup (p.Ile1313_Gln1314insTer)",
"text": "NM_000179.3(MSH6):c.3917_3938dup (p.Ile1313_Gln1314insTer) VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:breast_and_or_ovarian_cancer"... | {"gene": "MSH6", "disease": "Breast and/or ovarian cancer", "pathogenic_variants": ["NM_000179.3(MSH6):c.3917_3938dup (p.Ile1313_Gln1314insTer)"]} | 0.83666 | null |
no_dise_00609 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CDKN2A classified as Pathogenic or Likely Pathogenic for Acute lymphoid leukemia. | NM_000077.5(CDKN2A):c.151-6_151delinsC VARIANT_IN_GENE CDKN2A → NM_000077.5(CDKN2A):c.151-6_151delinsC VARIANT_HAS_CLINICAL_SIGNIFICANCE Acute lymphoid leukemia | {
"steps": [
{
"hop": 1,
"source_node_id": "CDKN2A",
"source_node_type": "GENE",
"source_node_label": "CDKN2A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000077... | NM_000077.5(CDKN2A):c.151-6_151delinsC | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CDKN2A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CDKN2A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_000077.5(CDKN2A):c.151-6_151delinsC",
"text": "NM_000077.5(CDKN2A):c.151-6_151delinsC VARIANT_IN_GENE CDKN2A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:acute_lymphoid_leukemia",
"text": "NM_000077.5(CDKN2A):c.151-6_... | {"gene": "CDKN2A", "disease": "Acute lymphoid leukemia", "pathogenic_variants": ["NM_000077.5(CDKN2A):c.174_185delinsGG (p.Val59fs)", "NM_000077.5(CDKN2A):c.151-6_151delinsC"]} | 0.83666 | null |
no_dise_00312 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in POLD1 classified as Pathogenic or Likely Pathogenic for Carcinoma of pancreas. | NM_002691.4(POLD1):c.3148del (p.Arg1050fs) VARIANT_IN_GENE POLD1 → NM_002691.4(POLD1):c.3148del (p.Arg1050fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Carcinoma of pancreas | {
"steps": [
{
"hop": 1,
"source_node_id": "POLD1",
"source_node_type": "GENE",
"source_node_label": "POLD1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_002691.4... | NM_002691.4(POLD1):c.3148del (p.Arg1050fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"POLD1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"POLD1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_002691.4(POLD1):c.3148del (p.Arg1050fs)",
"text": "NM_002691.4(POLD1):c.3148del (p.Arg1050fs) VARIANT_IN_GENE POLD1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:carcinoma_of_pancreas",
"text": "NM_002691.4(POLD1):c.31... | {"gene": "POLD1", "disease": "Carcinoma of pancreas", "pathogenic_variants": ["NM_002691.4(POLD1):c.3148del (p.Arg1050fs)"]} | 0.707107 | null |
no_dise_00127 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in TARDBP classified as Pathogenic or Likely Pathogenic for Amyotrophic lateral sclerosis type 10. | NM_007375.4(TARDBP):c.991C>A (p.Gln331Lys) VARIANT_IN_GENE TARDBP → NM_007375.4(TARDBP):c.991C>A (p.Gln331Lys) VARIANT_HAS_CLINICAL_SIGNIFICANCE Amyotrophic lateral sclerosis type 10 | {
"steps": [
{
"hop": 1,
"source_node_id": "TARDBP",
"source_node_type": "GENE",
"source_node_label": "TARDBP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007375... | NM_007375.4(TARDBP):c.991C>A (p.Gln331Lys) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"TARDBP\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"TARDBP\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_007375.4(TARDBP):c.991C>A (p.Gln331Lys)",
"text": "NM_007375.4(TARDBP):c.991C>A (p.Gln331Lys) VARIANT_IN_GENE TARDBP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:amyotrophic_lateral_sclerosis_type_10",
"text": "NM_007... | {"gene": "TARDBP", "disease": "Amyotrophic lateral sclerosis type 10", "pathogenic_variants": ["NM_007375.4(TARDBP):c.1123A>G (p.Ser375Gly)", "NM_007375.4(TARDBP):c.1035C>A (p.Asn345Lys)", "NM_007375.4(TARDBP):c.1028A>G (p.Gln343Arg)", "NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly)", "NM_007375.4(TARDBP):c.991C>A (p.Gln33... | 0.707107 | null |
no_dise_00335 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BCL11B classified as Pathogenic or Likely Pathogenic for BCL11B-related disorder. | NM_138576.4(BCL11B):c.2595del (p.Tyr866fs) VARIANT_IN_GENE BCL11B → NM_138576.4(BCL11B):c.2595del (p.Tyr866fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE BCL11B-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "BCL11B",
"source_node_type": "GENE",
"source_node_label": "BCL11B",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_138576... | NM_138576.4(BCL11B):c.2595del (p.Tyr866fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BCL11B\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BCL11B\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_138576.4(BCL11B):c.2595del (p.Tyr866fs)",
"text": "NM_138576.4(BCL11B):c.2595del (p.Tyr866fs) VARIANT_IN_GENE BCL11B",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:bcl11b_related_disorder",
"text": "NM_138576.4(BCL11B):... | {"gene": "BCL11B", "disease": "BCL11B-related disorder", "pathogenic_variants": ["NM_138576.4(BCL11B):c.756_765del (p.Gly253fs)", "NM_138576.4(BCL11B):c.2435_2436insAA (p.Val813fs)", "NM_138576.4(BCL11B):c.997G>A (p.Glu333Lys)", "NM_138576.4(BCL11B):c.2595del (p.Tyr866fs)", "NM_138576.4(BCL11B):c.1158C>A (p.Asn386Lys)"... | 0.83666 | null |
no_dise_00372 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in SOD1 classified as Pathogenic or Likely Pathogenic for Motor neuron disease. | NM_000454.5(SOD1):c.112G>A (p.Gly38Arg) VARIANT_IN_GENE SOD1 → NM_000454.5(SOD1):c.112G>A (p.Gly38Arg) VARIANT_HAS_CLINICAL_SIGNIFICANCE Motor neuron disease | {
"steps": [
{
"hop": 1,
"source_node_id": "SOD1",
"source_node_type": "GENE",
"source_node_label": "SOD1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000454.5(S... | NM_000454.5(SOD1):c.112G>A (p.Gly38Arg) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"SOD1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"SOD1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_000454.5(SOD1):c.112G>A (p.Gly38Arg)",
"text": "NM_000454.5(SOD1):c.112G>A (p.Gly38Arg) VARIANT_IN_GENE SOD1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:motor_neuron_disease",
"text": "NM_000454.5(SOD1):c.112G>A (p.G... | {"gene": "SOD1", "disease": "Motor neuron disease", "pathogenic_variants": ["NM_000454.5(SOD1):c.280G>C (p.Gly94Arg)", "NM_000454.5(SOD1):c.302A>G (p.Glu101Gly)", "NM_000454.5(SOD1):c.112G>A (p.Gly38Arg)", "NM_000454.5(SOD1):c.437C>A (p.Ala146Asp)"]} | 0.921954 | null |
no_dise_00074 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRAF classified as Pathogenic or Likely Pathogenic for Noonan syndrome 1. | NM_004333.6(BRAF):c.741T>A (p.Phe247Leu) VARIANT_IN_GENE BRAF → NM_004333.6(BRAF):c.741T>A (p.Phe247Leu) VARIANT_HAS_CLINICAL_SIGNIFICANCE Noonan syndrome 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004333.6(B... | NM_004333.6(BRAF):c.741T>A (p.Phe247Leu) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRAF\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRAF\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_004333.6(BRAF):c.741T>A (p.Phe247Leu)",
"text": "NM_004333.6(BRAF):c.741T>A (p.Phe247Leu) VARIANT_IN_GENE BRAF",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:noonan_syndrome_1",
"text": "NM_004333.6(BRAF):c.741T>A (p.Ph... | {"gene": "BRAF", "disease": "Noonan syndrome 1", "pathogenic_variants": ["NM_004333.6(BRAF):c.741T>A (p.Phe247Leu)"]} | 0.707107 | null |
no_dise_00034 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRAF classified as Pathogenic or Likely Pathogenic for Cardio-facio-cutaneous syndrome. | NM_004333.6(BRAF):c.721A>C (p.Thr241Pro) VARIANT_IN_GENE BRAF → NM_004333.6(BRAF):c.721A>C (p.Thr241Pro) VARIANT_HAS_CLINICAL_SIGNIFICANCE Cardio-facio-cutaneous syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "BRAF",
"source_node_type": "GENE",
"source_node_label": "BRAF",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004333.6(B... | NM_004333.6(BRAF):c.721A>C (p.Thr241Pro) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRAF\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRAF\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_004333.6(BRAF):c.721A>C (p.Thr241Pro)",
"text": "NM_004333.6(BRAF):c.721A>C (p.Thr241Pro) VARIANT_IN_GENE BRAF",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:cardio_facio_cutaneous_syndrome",
"text": "NM_004333.6(BRAF):... | {"gene": "BRAF", "disease": "Cardio-facio-cutaneous syndrome", "pathogenic_variants": ["NM_004333.6(BRAF):c.1783T>C (p.Phe595Leu)", "NM_004333.6(BRAF):c.785A>C (p.Gln262Pro)", "NM_004333.6(BRAF):c.1743T>A (p.Asn581Lys)", "NM_004333.6(BRAF):c.1720C>T (p.His574Tyr)", "NM_004333.6(BRAF):c.1460T>G (p.Val487Gly)", "NM_00433... | 0.921954 | null |
no_dise_00256 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in NOTCH1 classified as Pathogenic or Likely Pathogenic for Familial thoracic aortic aneurysm and aortic dissection. | NM_017617.5(NOTCH1):c.742G>C (p.Gly248Arg) VARIANT_IN_GENE NOTCH1 → NM_017617.5(NOTCH1):c.742G>C (p.Gly248Arg) VARIANT_HAS_CLINICAL_SIGNIFICANCE Familial thoracic aortic aneurysm and aortic dissection | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_017617... | NM_017617.5(NOTCH1):c.742G>C (p.Gly248Arg) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"NOTCH1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"NOTCH1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_017617.5(NOTCH1):c.742G>C (p.Gly248Arg)",
"text": "NM_017617.5(NOTCH1):c.742G>C (p.Gly248Arg) VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:familial_thoracic_aortic_aneurysm_and_aortic_dissection",
... | {"gene": "NOTCH1", "disease": "Familial thoracic aortic aneurysm and aortic dissection", "pathogenic_variants": ["NM_017617.5(NOTCH1):c.4348G>T (p.Glu1450Ter)", "NM_017617.5(NOTCH1):c.1896del (p.Thr633fs)", "NM_017617.5(NOTCH1):c.3129C>G (p.Tyr1043Ter)", "NM_017617.5(NOTCH1):c.3909_3919del (p.Cys1304fs)", "NM_017617.5(... | 0.83666 | null |
no_dise_00029 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PALB2 classified as Pathogenic or Likely Pathogenic for Inherited breast cancer and ovarian cancer. | NM_024675.4(PALB2):c.2730T>A (p.Tyr910Ter) VARIANT_IN_GENE PALB2 → NM_024675.4(PALB2):c.2730T>A (p.Tyr910Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inherited breast cancer and ovarian cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "PALB2",
"source_node_type": "GENE",
"source_node_label": "PALB2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_024675.4... | NM_024675.4(PALB2):c.2730T>A (p.Tyr910Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PALB2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PALB2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_024675.4(PALB2):c.2730T>A (p.Tyr910Ter)",
"text": "NM_024675.4(PALB2):c.2730T>A (p.Tyr910Ter) VARIANT_IN_GENE PALB2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inherited_breast_cancer_and_ovarian_cancer",
"text": "NM... | {"gene": "PALB2", "disease": "Inherited breast cancer and ovarian cancer", "pathogenic_variants": ["NM_024675.4(PALB2):c.764_767dup (p.Ser256delinsArgTer)", "NM_024675.4(PALB2):c.1486_1487del (p.Glu495_Asp496insTer)", "NM_024675.4(PALB2):c.2556del (p.Gly853fs)", "NM_024675.4(PALB2):c.1458del (p.Val487fs)", "NM_024675.4... | 0.921954 | null |
no_dise_00103 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in ACTB classified as Pathogenic or Likely Pathogenic for Dystonia 22, juvenile-onset. | GRCh37/hg19 7p22.1(chr7:5521357-5569119)x1 VARIANT_IN_GENE ACTB → GRCh37/hg19 7p22.1(chr7:5521357-5569119)x1 VARIANT_HAS_CLINICAL_SIGNIFICANCE Dystonia 22, juvenile-onset | {
"steps": [
{
"hop": 1,
"source_node_id": "ACTB",
"source_node_type": "GENE",
"source_node_label": "ACTB",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "GRCh37/hg19 7... | GRCh37/hg19 7p22.1(chr7:5521357-5569119)x1 | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"ACTB\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"ACTB\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "GRCh37/hg19 7p22.1(chr7:5521357-5569119)x1",
"text": "GRCh37/hg19 7p22.1(chr7:5521357-5569119)x1 VARIANT_IN_GENE ACTB",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:dystonia_22_juvenile_onset",
"text": "GRCh37/hg19 7p22.1(... | {"gene": "ACTB", "disease": "Dystonia 22, juvenile-onset", "pathogenic_variants": ["GRCh37/hg19 7p22.1(chr7:5521357-5569119)x1"]} | 0.707107 | null |
no_dise_00121 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in DNMT3A classified as Pathogenic or Likely Pathogenic for Heyn-Sproul-Jackson syndrome. | NM_022552.5(DNMT3A):c.916T>C (p.Trp306Arg) VARIANT_IN_GENE DNMT3A → NM_022552.5(DNMT3A):c.916T>C (p.Trp306Arg) VARIANT_HAS_CLINICAL_SIGNIFICANCE Heyn-Sproul-Jackson syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "DNMT3A",
"source_node_type": "GENE",
"source_node_label": "DNMT3A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_022552... | NM_022552.5(DNMT3A):c.916T>C (p.Trp306Arg) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"DNMT3A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"DNMT3A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_022552.5(DNMT3A):c.916T>C (p.Trp306Arg)",
"text": "NM_022552.5(DNMT3A):c.916T>C (p.Trp306Arg) VARIANT_IN_GENE DNMT3A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:heyn_sproul_jackson_syndrome",
"text": "NM_022552.5(DNM... | {"gene": "DNMT3A", "disease": "Heyn-Sproul-Jackson syndrome", "pathogenic_variants": ["NM_022552.5(DNMT3A):c.1092dup (p.Tyr365fs)", "NM_022552.5(DNMT3A):c.1012_1014+3del", "NM_022552.5(DNMT3A):c.988T>C (p.Trp330Arg)", "NM_022552.5(DNMT3A):c.916T>C (p.Trp306Arg)", "NM_022552.5(DNMT3A):c.905G>C (p.Gly302Ala)"]} | 0.83666 | null |
no_dise_00626 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in SPTLC2 classified as Pathogenic or Likely Pathogenic for Hereditary neuropathy or pain disorder. | NM_004863.4(SPTLC2):c.547C>T (p.Arg183Trp) VARIANT_IN_GENE SPTLC2 → NM_004863.4(SPTLC2):c.547C>T (p.Arg183Trp) VARIANT_HAS_CLINICAL_SIGNIFICANCE Hereditary neuropathy or pain disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "SPTLC2",
"source_node_type": "GENE",
"source_node_label": "SPTLC2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004863... | NM_004863.4(SPTLC2):c.547C>T (p.Arg183Trp) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"SPTLC2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"SPTLC2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_004863.4(SPTLC2):c.547C>T (p.Arg183Trp)",
"text": "NM_004863.4(SPTLC2):c.547C>T (p.Arg183Trp) VARIANT_IN_GENE SPTLC2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hereditary_neuropathy_or_pain_disorder",
"text": "NM_00... | {"gene": "SPTLC2", "disease": "Hereditary neuropathy or pain disorder", "pathogenic_variants": ["NM_004863.4(SPTLC2):c.547C>T (p.Arg183Trp)"]} | 0.921954 | null |
no_dise_00076 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PSEN1 classified as Pathogenic or Likely Pathogenic for Telangiectasia, hereditary hemorrhagic, type 1. | NM_000021.4(PSEN1):c.308T>A (p.Val103Asp) VARIANT_IN_GENE PSEN1 → NM_000021.4(PSEN1):c.308T>A (p.Val103Asp) VARIANT_HAS_CLINICAL_SIGNIFICANCE Telangiectasia, hereditary hemorrhagic, type 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "PSEN1",
"source_node_type": "GENE",
"source_node_label": "PSEN1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000021.4... | NM_000021.4(PSEN1):c.308T>A (p.Val103Asp) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PSEN1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PSEN1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_000021.4(PSEN1):c.308T>A (p.Val103Asp)",
"text": "NM_000021.4(PSEN1):c.308T>A (p.Val103Asp) VARIANT_IN_GENE PSEN1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:telangiectasia_hereditary_hemorrhagic_type_1",
"text": "NM... | {"gene": "PSEN1", "disease": "Telangiectasia, hereditary hemorrhagic, type 1", "pathogenic_variants": ["NM_000021.4(PSEN1):c.308T>A (p.Val103Asp)"]} | 0.83666 | null |
no_dise_00106 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BIN1 classified as Pathogenic or Likely Pathogenic for Inborn genetic diseases. | NM_139343.3(BIN1):c.91C>T (p.Gln31Ter) VARIANT_IN_GENE BIN1 → NM_139343.3(BIN1):c.91C>T (p.Gln31Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inborn genetic diseases | {
"steps": [
{
"hop": 1,
"source_node_id": "BIN1",
"source_node_type": "GENE",
"source_node_label": "BIN1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_139343.3(B... | NM_139343.3(BIN1):c.91C>T (p.Gln31Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BIN1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BIN1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_139343.3(BIN1):c.91C>T (p.Gln31Ter)",
"text": "NM_139343.3(BIN1):c.91C>T (p.Gln31Ter) VARIANT_IN_GENE BIN1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inborn_genetic_diseases",
"text": "NM_139343.3(BIN1):c.91C>T (p.G... | {"gene": "BIN1", "disease": "Inborn genetic diseases", "pathogenic_variants": ["NM_139343.3(BIN1):c.91C>T (p.Gln31Ter)"]} | 0.83666 | null |
no_dise_00283 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in FGFR1 classified as Pathogenic or Likely Pathogenic for Pfeiffer syndrome. | NM_023110.3(FGFR1):c.1946del (p.His649fs) VARIANT_IN_GENE FGFR1 → NM_023110.3(FGFR1):c.1946del (p.His649fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Pfeiffer syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "FGFR1",
"source_node_type": "GENE",
"source_node_label": "FGFR1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_023110.3... | NM_023110.3(FGFR1):c.1946del (p.His649fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"FGFR1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"FGFR1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_023110.3(FGFR1):c.1946del (p.His649fs)",
"text": "NM_023110.3(FGFR1):c.1946del (p.His649fs) VARIANT_IN_GENE FGFR1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:pfeiffer_syndrome",
"text": "NM_023110.3(FGFR1):c.1946del ... | {"gene": "FGFR1", "disease": "Pfeiffer syndrome", "pathogenic_variants": ["NM_023110.3(FGFR1):c.570del (p.Trp190fs)", "NM_023110.3(FGFR1):c.74del (p.Pro25fs)", "NM_023110.3(FGFR1):c.494del (p.Leu165fs)", "NM_023110.3(FGFR1):c.831dup (p.Lys278Ter)", "NM_023110.3(FGFR1):c.1231C>T (p.Gln411Ter)", "NM_023110.3(FGFR1):c.188... | 0.83666 | null |
no_dise_00556 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PALB2 classified as Pathogenic or Likely Pathogenic for PALB2-related disorder. | NM_024675.4(PALB2):c.2053A>T (p.Lys685Ter) VARIANT_IN_GENE PALB2 → NM_024675.4(PALB2):c.2053A>T (p.Lys685Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE PALB2-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "PALB2",
"source_node_type": "GENE",
"source_node_label": "PALB2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_024675.4... | NM_024675.4(PALB2):c.2053A>T (p.Lys685Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PALB2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PALB2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_024675.4(PALB2):c.2053A>T (p.Lys685Ter)",
"text": "NM_024675.4(PALB2):c.2053A>T (p.Lys685Ter) VARIANT_IN_GENE PALB2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:palb2_related_disorder",
"text": "NM_024675.4(PALB2):c.2... | {"gene": "PALB2", "disease": "PALB2-related disorder", "pathogenic_variants": ["NM_024675.4(PALB2):c.2053A>T (p.Lys685Ter)", "NM_024675.4(PALB2):c.454A>T (p.Lys152Ter)", "NM_024675.4(PALB2):c.934del (p.Ser312fs)", "NM_024675.4(PALB2):c.1553C>G (p.Ser518Ter)", "NM_024675.4(PALB2):c.2835-1G>A", "NM_024675.4(PALB2):c.3507... | 0.707107 | null |
no_dise_00361 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in TUBA4A classified as Pathogenic or Likely Pathogenic for Amyotrophic lateral sclerosis type 22. | NM_006000.3(TUBA4A):c.959G>A (p.Arg320His) VARIANT_IN_GENE TUBA4A → NM_006000.3(TUBA4A):c.959G>A (p.Arg320His) VARIANT_HAS_CLINICAL_SIGNIFICANCE Amyotrophic lateral sclerosis type 22 | {
"steps": [
{
"hop": 1,
"source_node_id": "TUBA4A",
"source_node_type": "GENE",
"source_node_label": "TUBA4A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_006000... | NM_006000.3(TUBA4A):c.959G>A (p.Arg320His) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"TUBA4A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"TUBA4A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_006000.3(TUBA4A):c.959G>A (p.Arg320His)",
"text": "NM_006000.3(TUBA4A):c.959G>A (p.Arg320His) VARIANT_IN_GENE TUBA4A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:amyotrophic_lateral_sclerosis_type_22",
"text": "NM_006... | {"gene": "TUBA4A", "disease": "Amyotrophic lateral sclerosis type 22", "pathogenic_variants": ["NM_006000.3(TUBA4A):c.190del (p.Arg64fs)", "NM_006000.3(TUBA4A):c.433A>C (p.Thr145Pro)", "NM_006000.3(TUBA4A):c.1220G>A (p.Trp407Ter)", "NM_006000.3(TUBA4A):c.959G>A (p.Arg320His)", "NM_006000.3(TUBA4A):c.313C>T (p.Arg105Cys... | 0.707107 | null |
no_dise_00429 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in MTOR classified as Pathogenic or Likely Pathogenic for MTOR-related disorder. | NM_004958.4(MTOR):c.6306C>A (p.Asp2102Glu) VARIANT_IN_GENE MTOR → NM_004958.4(MTOR):c.6306C>A (p.Asp2102Glu) VARIANT_HAS_CLINICAL_SIGNIFICANCE MTOR-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "MTOR",
"source_node_type": "GENE",
"source_node_label": "MTOR",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004958.4(M... | NM_004958.4(MTOR):c.6306C>A (p.Asp2102Glu) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"MTOR\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"MTOR\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_004958.4(MTOR):c.6306C>A (p.Asp2102Glu)",
"text": "NM_004958.4(MTOR):c.6306C>A (p.Asp2102Glu) VARIANT_IN_GENE MTOR",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:mtor_related_disorder",
"text": "NM_004958.4(MTOR):c.6306... | {"gene": "MTOR", "disease": "MTOR-related disorder", "pathogenic_variants": ["NM_004958.4(MTOR):c.6306C>A (p.Asp2102Glu)"]} | 0.83666 | null |
no_dise_00059 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PSEN1 classified as Pathogenic or Likely Pathogenic for Alzheimer disease 4. | NM_000021.4(PSEN1):c.869-1624_956-2452del VARIANT_IN_GENE PSEN1 → NM_000021.4(PSEN1):c.869-1624_956-2452del VARIANT_HAS_CLINICAL_SIGNIFICANCE Alzheimer disease 4 | {
"steps": [
{
"hop": 1,
"source_node_id": "PSEN1",
"source_node_type": "GENE",
"source_node_label": "PSEN1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000021.4... | NM_000021.4(PSEN1):c.869-1624_956-2452del | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PSEN1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PSEN1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_000021.4(PSEN1):c.869-1624_956-2452del",
"text": "NM_000021.4(PSEN1):c.869-1624_956-2452del VARIANT_IN_GENE PSEN1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:alzheimer_disease_4",
"text": "NM_000021.4(PSEN1):c.869-16... | {"gene": "PSEN1", "disease": "Alzheimer disease 4", "pathogenic_variants": ["NM_000021.4(PSEN1):c.869-1624_956-2452del"]} | 0.707107 | null |
no_dise_00509 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CDKN2A classified as Pathogenic or Likely Pathogenic for Hereditary cancer-predisposing syndrome. | NM_000077.5(CDKN2A):c.189del (p.Leu64fs) VARIANT_IN_GENE CDKN2A → NM_000077.5(CDKN2A):c.189del (p.Leu64fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Hereditary cancer-predisposing syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "CDKN2A",
"source_node_type": "GENE",
"source_node_label": "CDKN2A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000077... | NM_000077.5(CDKN2A):c.189del (p.Leu64fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CDKN2A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CDKN2A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_000077.5(CDKN2A):c.189del (p.Leu64fs)",
"text": "NM_000077.5(CDKN2A):c.189del (p.Leu64fs) VARIANT_IN_GENE CDKN2A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hereditary_cancer_predisposing_syndrome",
"text": "NM_00007... | {"gene": "CDKN2A", "disease": "Hereditary cancer-predisposing syndrome", "pathogenic_variants": ["NM_000077.5(CDKN2A):c.171_172delinsTT (p.Arg58Ter)", "NM_000077.5(CDKN2A):c.328_329insA (p.Trp110Ter)", "NM_000077.5(CDKN2A):c.135_138del (p.Arg46fs)", "NM_000077.5(CDKN2A):c.98_150+1488del", "NM_000077.5(CDKN2A):c.274del ... | 0.921954 | null |
no_dise_00060 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in FGFR1 classified as Pathogenic or Likely Pathogenic for Hartsfield-Bixler-Demyer syndrome. | NM_023110.3(FGFR1):c.1601TGA[1] (p.Met535del) VARIANT_IN_GENE FGFR1 → NM_023110.3(FGFR1):c.1601TGA[1] (p.Met535del) VARIANT_HAS_CLINICAL_SIGNIFICANCE Hartsfield-Bixler-Demyer syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "FGFR1",
"source_node_type": "GENE",
"source_node_label": "FGFR1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_023110.3... | NM_023110.3(FGFR1):c.1601TGA[1] (p.Met535del) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"FGFR1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"FGFR1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_023110.3(FGFR1):c.1601TGA[1] (p.Met535del)",
"text": "NM_023110.3(FGFR1):c.1601TGA[1] (p.Met535del) VARIANT_IN_GENE FGFR1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hartsfield_bixler_demyer_syndrome",
"text": "NM_02... | {"gene": "FGFR1", "disease": "Hartsfield-Bixler-Demyer syndrome", "pathogenic_variants": ["NM_023110.3(FGFR1):c.1881G>C (p.Arg627Ser)", "NM_023110.3(FGFR1):c.1996T>C (p.Trp666Arg)", "NM_023110.3(FGFR1):c.1869C>G (p.Asp623Glu)", "NM_023110.3(FGFR1):c.1921G>A (p.Asp641Asn)", "NM_023110.3(FGFR1):c.1604T>A (p.Met535Lys)", ... | 0.921954 | null |
no_dise_00464 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in MSH6 classified as Pathogenic or Likely Pathogenic for MSH6-related disorder. | NM_000179.3(MSH6):c.1993G>T (p.Glu665Ter) VARIANT_IN_GENE MSH6 → NM_000179.3(MSH6):c.1993G>T (p.Glu665Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE MSH6-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH6",
"source_node_type": "GENE",
"source_node_label": "MSH6",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000179.3(M... | NM_000179.3(MSH6):c.1993G>T (p.Glu665Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"MSH6\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"MSH6\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_000179.3(MSH6):c.1993G>T (p.Glu665Ter)",
"text": "NM_000179.3(MSH6):c.1993G>T (p.Glu665Ter) VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:msh6_related_disorder",
"text": "NM_000179.3(MSH6):c.1993G>... | {"gene": "MSH6", "disease": "MSH6-related disorder", "pathogenic_variants": ["NM_000179.3(MSH6):c.160_196dup (p.Pro66fs)", "NM_000179.3(MSH6):c.1993G>T (p.Glu665Ter)"]} | 0.921954 | null |
no_dise_00155 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in DDX41 classified as Pathogenic or Likely Pathogenic for Inborn genetic diseases. | NM_016222.4(DDX41):c.325C>T (p.Gln109Ter) VARIANT_IN_GENE DDX41 → NM_016222.4(DDX41):c.325C>T (p.Gln109Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inborn genetic diseases | {
"steps": [
{
"hop": 1,
"source_node_id": "DDX41",
"source_node_type": "GENE",
"source_node_label": "DDX41",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_016222.4... | NM_016222.4(DDX41):c.325C>T (p.Gln109Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"DDX41\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"DDX41\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_016222.4(DDX41):c.325C>T (p.Gln109Ter)",
"text": "NM_016222.4(DDX41):c.325C>T (p.Gln109Ter) VARIANT_IN_GENE DDX41",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inborn_genetic_diseases",
"text": "NM_016222.4(DDX41):c.32... | {"gene": "DDX41", "disease": "Inborn genetic diseases", "pathogenic_variants": ["NM_016222.4(DDX41):c.304A>T (p.Lys102Ter)", "NM_016222.4(DDX41):c.622C>T (p.Gln208Ter)", "NM_016222.4(DDX41):c.116del (p.Leu39fs)", "NM_016222.4(DDX41):c.1233_1234dup (p.Val412fs)", "NM_016222.4(DDX41):c.1504C>T (p.Gln502Ter)", "NM_016222.... | 0.83666 | null |
no_dise_00004 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in FUS classified as Pathogenic or Likely Pathogenic for Amyotrophic lateral sclerosis 6, autosomal recessive. | NM_004960.4(FUS):c.1551C>G (p.His517Gln) VARIANT_IN_GENE FUS → NM_004960.4(FUS):c.1551C>G (p.His517Gln) VARIANT_HAS_CLINICAL_SIGNIFICANCE Amyotrophic lateral sclerosis 6, autosomal recessive | {
"steps": [
{
"hop": 1,
"source_node_id": "FUS",
"source_node_type": "GENE",
"source_node_label": "FUS",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004960.4(FUS... | NM_004960.4(FUS):c.1551C>G (p.His517Gln) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"FUS\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"FUS\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_004960.4(FUS):c.1551C>G (p.His517Gln)",
"text": "NM_004960.4(FUS):c.1551C>G (p.His517Gln) VARIANT_IN_GENE FUS",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:amyotrophic_lateral_sclerosis_6_autosomal_recessive",
"text": ... | {"gene": "FUS", "disease": "Amyotrophic lateral sclerosis 6, autosomal recessive", "pathogenic_variants": ["NM_004960.4(FUS):c.1551C>G (p.His517Gln)"]} | 0.707107 | null |
no_dise_00511 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in BRCA1 classified as Pathogenic or Likely Pathogenic for Breast and/or ovarian cancer. | NM_007294.4(BRCA1):c.53T>A (p.Met18Lys) VARIANT_IN_GENE BRCA1 → NM_007294.4(BRCA1):c.53T>A (p.Met18Lys) VARIANT_HAS_CLINICAL_SIGNIFICANCE Breast and/or ovarian cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "BRCA1",
"source_node_type": "GENE",
"source_node_label": "BRCA1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_007294.4... | NM_007294.4(BRCA1):c.53T>A (p.Met18Lys) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"BRCA1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"BRCA1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_007294.4(BRCA1):c.53T>A (p.Met18Lys)",
"text": "NM_007294.4(BRCA1):c.53T>A (p.Met18Lys) VARIANT_IN_GENE BRCA1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:breast_and_or_ovarian_cancer",
"text": "NM_007294.4(BRCA1):c.5... | {"gene": "BRCA1", "disease": "Breast and/or ovarian cancer", "pathogenic_variants": ["NM_007294.4(BRCA1):c.5332_5332+6delinsT", "NM_007294.4(BRCA1):c.3690dup (p.Phe1231fs)", "NM_007294.4(BRCA1):c.5116G>C (p.Gly1706Arg)", "NM_007294.4(BRCA1):c.53T>A (p.Met18Lys)"]} | 0.921954 | null |
no_dise_00496 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PMS2 classified as Pathogenic or Likely Pathogenic for Hereditary cancer-predisposing syndrome. | NM_000535.7(PMS2):c.2175-2A>C VARIANT_IN_GENE PMS2 → NM_000535.7(PMS2):c.2175-2A>C VARIANT_HAS_CLINICAL_SIGNIFICANCE Hereditary cancer-predisposing syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "PMS2",
"source_node_type": "GENE",
"source_node_label": "PMS2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000535.7(P... | NM_000535.7(PMS2):c.2175-2A>C | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PMS2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PMS2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_000535.7(PMS2):c.2175-2A>C",
"text": "NM_000535.7(PMS2):c.2175-2A>C VARIANT_IN_GENE PMS2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hereditary_cancer_predisposing_syndrome",
"text": "NM_000535.7(PMS2):c.2175-2A>C VA... | {"gene": "PMS2", "disease": "Hereditary cancer-predisposing syndrome", "pathogenic_variants": ["NM_000535.7(PMS2):c.674_677dup (p.Asn226fs)", "NM_000535.7(PMS2):c.860_864del (p.Arg287fs)", "NM_000535.7(PMS2):c.1456dup (p.Asp486fs)", "NM_000535.7(PMS2):c.1240dup (p.Asp414fs)", "NM_000535.7(PMS2):c.2309T>A (p.Leu770Ter)"... | 0.83666 | null |
no_dise_00040 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in FUS classified as Pathogenic or Likely Pathogenic for Tremor, hereditary essential, 4. | NM_004960.4(FUS):c.1561C>G (p.Arg521Gly) VARIANT_IN_GENE FUS → NM_004960.4(FUS):c.1561C>G (p.Arg521Gly) VARIANT_HAS_CLINICAL_SIGNIFICANCE Tremor, hereditary essential, 4 | {
"steps": [
{
"hop": 1,
"source_node_id": "FUS",
"source_node_type": "GENE",
"source_node_label": "FUS",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004960.4(FUS... | NM_004960.4(FUS):c.1561C>G (p.Arg521Gly) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"FUS\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"FUS\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_004960.4(FUS):c.1561C>G (p.Arg521Gly)",
"text": "NM_004960.4(FUS):c.1561C>G (p.Arg521Gly) VARIANT_IN_GENE FUS",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:tremor_hereditary_essential_4",
"text": "NM_004960.4(FUS):c.15... | {"gene": "FUS", "disease": "Tremor, hereditary essential, 4", "pathogenic_variants": ["NM_004960.4(FUS):c.1441C>T (p.Arg481Ter)", "NM_004960.4(FUS):c.1573C>A (p.Pro525Thr)", "NM_004960.4(FUS):c.1500dup (p.Gly501fs)", "NM_004960.4(FUS):c.1509_1510dup (p.Gly504fs)", "NM_004960.4(FUS):c.1394-2del", "NM_004960.4(FUS):c.868... | 0.921954 | null |
no_dise_00595 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in MSH6 classified as Pathogenic or Likely Pathogenic for Lynch-like syndrome. | NM_000179.3(MSH6):c.1372C>A (p.His458Asn) VARIANT_IN_GENE MSH6 → NM_000179.3(MSH6):c.1372C>A (p.His458Asn) VARIANT_HAS_CLINICAL_SIGNIFICANCE Lynch-like syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH6",
"source_node_type": "GENE",
"source_node_label": "MSH6",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000179.3(M... | NM_000179.3(MSH6):c.1372C>A (p.His458Asn) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"MSH6\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"MSH6\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_000179.3(MSH6):c.1372C>A (p.His458Asn)",
"text": "NM_000179.3(MSH6):c.1372C>A (p.His458Asn) VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:lynch_like_syndrome",
"text": "NM_000179.3(MSH6):c.1372C>A ... | {"gene": "MSH6", "disease": "Lynch-like syndrome", "pathogenic_variants": ["NM_000179.3(MSH6):c.1372C>A (p.His458Asn)"]} | 0.707107 | null |
no_dise_00025 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in NOTCH1 classified as Pathogenic or Likely Pathogenic for NOTCH1-related disorder. | NM_017617.5(NOTCH1):c.5078T>C (p.Phe1693Ser) VARIANT_IN_GENE NOTCH1 → NM_017617.5(NOTCH1):c.5078T>C (p.Phe1693Ser) VARIANT_HAS_CLINICAL_SIGNIFICANCE NOTCH1-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "NOTCH1",
"source_node_type": "GENE",
"source_node_label": "NOTCH1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_017617... | NM_017617.5(NOTCH1):c.5078T>C (p.Phe1693Ser) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"NOTCH1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"NOTCH1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_017617.5(NOTCH1):c.5078T>C (p.Phe1693Ser)",
"text": "NM_017617.5(NOTCH1):c.5078T>C (p.Phe1693Ser) VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:notch1_related_disorder",
"text": "NM_017617.5(NOTC... | {"gene": "NOTCH1", "disease": "NOTCH1-related disorder", "pathogenic_variants": ["NM_017617.5(NOTCH1):c.3170del (p.Gln1057fs)", "NM_017617.5(NOTCH1):c.5078T>C (p.Phe1693Ser)", "NM_017617.5(NOTCH1):c.2436del (p.Tyr813fs)", "NM_017617.5(NOTCH1):c.4315_4318dup (p.Ile1440fs)", "NM_017617.5(NOTCH1):c.2536C>T (p.Gln846Ter)",... | 0.707107 | null |
no_dise_00420 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in RET classified as Pathogenic or Likely Pathogenic for Pheochromocytoma. | NM_020975.6(RET):c.1996A>G (p.Lys666Glu) VARIANT_IN_GENE RET → NM_020975.6(RET):c.1996A>G (p.Lys666Glu) VARIANT_HAS_CLINICAL_SIGNIFICANCE Pheochromocytoma | {
"steps": [
{
"hop": 1,
"source_node_id": "RET",
"source_node_type": "GENE",
"source_node_label": "RET",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_020975.6(RET... | NM_020975.6(RET):c.1996A>G (p.Lys666Glu) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"RET\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"RET\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_020975.6(RET):c.1996A>G (p.Lys666Glu)",
"text": "NM_020975.6(RET):c.1996A>G (p.Lys666Glu) VARIANT_IN_GENE RET",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:pheochromocytoma",
"text": "NM_020975.6(RET):c.1996A>G (p.Lys6... | {"gene": "RET", "disease": "Pheochromocytoma", "pathogenic_variants": ["NM_020975.6(RET):c.1996A>G (p.Lys666Glu)"]} | 0.921954 | null |
no_dise_00012 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in RAD51D classified as Pathogenic or Likely Pathogenic for Malignant tumor of breast. | NM_002878.4(RAD51D):c.738+402_*1465del VARIANT_IN_GENE RAD51D → NM_002878.4(RAD51D):c.738+402_*1465del VARIANT_HAS_CLINICAL_SIGNIFICANCE Malignant tumor of breast | {
"steps": [
{
"hop": 1,
"source_node_id": "RAD51D",
"source_node_type": "GENE",
"source_node_label": "RAD51D",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_002878... | NM_002878.4(RAD51D):c.738+402_*1465del | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"RAD51D\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"RAD51D\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_002878.4(RAD51D):c.738+402_*1465del",
"text": "NM_002878.4(RAD51D):c.738+402_*1465del VARIANT_IN_GENE RAD51D",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:malignant_tumor_of_breast",
"text": "NM_002878.4(RAD51D):c.738+... | {"gene": "RAD51D", "disease": "Malignant tumor of breast", "pathogenic_variants": ["NM_002878.4(RAD51D):c.738+402_*1465del"]} | 0.83666 | null |
no_dise_00013 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in DCTN1 classified as Pathogenic or Likely Pathogenic for Amyotrophic lateral sclerosis type 1. | NM_004082.5(DCTN1):c.3823C>T (p.Arg1275Cys) VARIANT_IN_GENE DCTN1 → NM_004082.5(DCTN1):c.3823C>T (p.Arg1275Cys) VARIANT_HAS_CLINICAL_SIGNIFICANCE Amyotrophic lateral sclerosis type 1 | {
"steps": [
{
"hop": 1,
"source_node_id": "DCTN1",
"source_node_type": "GENE",
"source_node_label": "DCTN1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004082.5... | NM_004082.5(DCTN1):c.3823C>T (p.Arg1275Cys) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"DCTN1\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"DCTN1\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_004082.5(DCTN1):c.3823C>T (p.Arg1275Cys)",
"text": "NM_004082.5(DCTN1):c.3823C>T (p.Arg1275Cys) VARIANT_IN_GENE DCTN1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:amyotrophic_lateral_sclerosis_type_1",
"text": "NM_004... | {"gene": "DCTN1", "disease": "Amyotrophic lateral sclerosis type 1", "pathogenic_variants": ["NM_004082.5(DCTN1):c.175G>C (p.Gly59Arg)", "NM_004082.5(DCTN1):c.175G>A (p.Gly59Ser)", "NM_004082.5(DCTN1):c.3823C>T (p.Arg1275Cys)", "NM_004082.5(DCTN1):c.232T>C (p.Tyr78His)"]} | 0.83666 | null |
no_dise_00159 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in FAT4 classified as Pathogenic or Likely Pathogenic for Van Maldergem syndrome. | NM_001291303.3(FAT4):c.6700C>T (p.Arg2234Ter) VARIANT_IN_GENE FAT4 → NM_001291303.3(FAT4):c.6700C>T (p.Arg2234Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Van Maldergem syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "FAT4",
"source_node_type": "GENE",
"source_node_label": "FAT4",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001291303.... | NM_001291303.3(FAT4):c.6700C>T (p.Arg2234Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"FAT4\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"FAT4\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_001291303.3(FAT4):c.6700C>T (p.Arg2234Ter)",
"text": "NM_001291303.3(FAT4):c.6700C>T (p.Arg2234Ter) VARIANT_IN_GENE FAT4",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:van_maldergem_syndrome",
"text": "NM_001291303.3(FA... | {"gene": "FAT4", "disease": "Van Maldergem syndrome", "pathogenic_variants": ["NM_001291303.3(FAT4):c.6700C>T (p.Arg2234Ter)"]} | 0.921954 | null |
no_dise_00354 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in CREBBP classified as Pathogenic or Likely Pathogenic for CREBBP-related disorder. | NM_004380.3(CREBBP):c.3054del (p.Arg1018fs) VARIANT_IN_GENE CREBBP → NM_004380.3(CREBBP):c.3054del (p.Arg1018fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE CREBBP-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "CREBBP",
"source_node_type": "GENE",
"source_node_label": "CREBBP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004380... | NM_004380.3(CREBBP):c.3054del (p.Arg1018fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"CREBBP\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"CREBBP\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Br... | [
{
"source_db": "ClinVar",
"source_id": "NM_004380.3(CREBBP):c.3054del (p.Arg1018fs)",
"text": "NM_004380.3(CREBBP):c.3054del (p.Arg1018fs) VARIANT_IN_GENE CREBBP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:crebbp_related_disorder",
"text": "NM_004380.3(CREBBP... | {"gene": "CREBBP", "disease": "CREBBP-related disorder", "pathogenic_variants": ["NM_004380.3(CREBBP):c.2064_2077del (p.Gly689fs)", "NM_004380.3(CREBBP):c.5948dup (p.Gly1984fs)", "NM_004380.3(CREBBP):c.4944del (p.Ile1649fs)", "NM_004380.3(CREBBP):c.223C>T (p.Arg75Ter)", "NM_004380.3(CREBBP):c.4890+1G>A", "NM_004380.3(C... | 0.707107 | null |
no_dise_00520 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in AXIN2 classified as Pathogenic or Likely Pathogenic for AXIN2-related attenuated familial adenomatous polyposis. | NM_004655.4(AXIN2):c.2062_2063del (p.Leu688fs) VARIANT_IN_GENE AXIN2 → NM_004655.4(AXIN2):c.2062_2063del (p.Leu688fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE AXIN2-related attenuated familial adenomatous polyposis | {
"steps": [
{
"hop": 1,
"source_node_id": "AXIN2",
"source_node_type": "GENE",
"source_node_label": "AXIN2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004655.4... | NM_004655.4(AXIN2):c.2062_2063del (p.Leu688fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"AXIN2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"AXIN2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_004655.4(AXIN2):c.2062_2063del (p.Leu688fs)",
"text": "NM_004655.4(AXIN2):c.2062_2063del (p.Leu688fs) VARIANT_IN_GENE AXIN2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:axin2_related_attenuated_familial_adenomatous_polypo... | {"gene": "AXIN2", "disease": "AXIN2-related attenuated familial adenomatous polyposis", "pathogenic_variants": ["NM_004655.4(AXIN2):c.2062_2063del (p.Leu688fs)", "NM_004655.4(AXIN2):c.1989G>A (p.Trp663Ter)", "NM_004655.4(AXIN2):c.2041C>T (p.Gln681Ter)", "NM_004655.4(AXIN2):c.1647T>G (p.Tyr549Ter)", "NM_004655.4(AXIN2):... | 0.921954 | null |
no_dise_00206 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in KDM6A classified as Pathogenic or Likely Pathogenic for KDM6A-related disorder. | NM_001291415.2(KDM6A):c.1083_1084del (p.Leu361_Tyr362insTer) VARIANT_IN_GENE KDM6A → NM_001291415.2(KDM6A):c.1083_1084del (p.Leu361_Tyr362insTer) VARIANT_HAS_CLINICAL_SIGNIFICANCE KDM6A-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "KDM6A",
"source_node_type": "GENE",
"source_node_label": "KDM6A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_00129141... | NM_001291415.2(KDM6A):c.1083_1084del (p.Leu361_Tyr362insTer) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"KDM6A\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"KDM6A\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_001291415.2(KDM6A):c.1083_1084del (p.Leu361_Tyr362insTer)",
"text": "NM_001291415.2(KDM6A):c.1083_1084del (p.Leu361_Tyr362insTer) VARIANT_IN_GENE KDM6A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:kdm6a_related_disorder",... | {"gene": "KDM6A", "disease": "KDM6A-related disorder", "pathogenic_variants": ["NM_001291415.2(KDM6A):c.2605del (p.Ser869fs)", "NM_001291415.2(KDM6A):c.1083_1084del (p.Leu361_Tyr362insTer)"]} | 0.83666 | null |
no_dise_00325 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in GRN classified as Pathogenic or Likely Pathogenic for GRN-related disorder. | NM_002087.4(GRN):c.347C>A (p.Ser116Ter) VARIANT_IN_GENE GRN → NM_002087.4(GRN):c.347C>A (p.Ser116Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE GRN-related disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "GRN",
"source_node_type": "GENE",
"source_node_label": "GRN",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_002087.4(GRN... | NM_002087.4(GRN):c.347C>A (p.Ser116Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"GRN\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"GRN\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_002087.4(GRN):c.347C>A (p.Ser116Ter)",
"text": "NM_002087.4(GRN):c.347C>A (p.Ser116Ter) VARIANT_IN_GENE GRN",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:grn_related_disorder",
"text": "NM_002087.4(GRN):c.347C>A (p.Ser... | {"gene": "GRN", "disease": "GRN-related disorder", "pathogenic_variants": ["NM_002087.4(GRN):c.1535del (p.Pro512fs)", "NM_002087.4(GRN):c.347C>A (p.Ser116Ter)", "NM_002087.4(GRN):c.1429_1430dup (p.Asp477fs)", "NM_002087.4(GRN):c.388_391del (p.Gln130fs)", "NM_002087.4(GRN):c.900_901dup (p.Ser301fs)"]} | 0.83666 | null |
no_dise_00289 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in FAT4 classified as Pathogenic or Likely Pathogenic for Hennekam lymphangiectasia-lymphedema syndrome 2. | NM_001291303.3(FAT4):c.14610del (p.Lys4871fs) VARIANT_IN_GENE FAT4 → NM_001291303.3(FAT4):c.14610del (p.Lys4871fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Hennekam lymphangiectasia-lymphedema syndrome 2 | {
"steps": [
{
"hop": 1,
"source_node_id": "FAT4",
"source_node_type": "GENE",
"source_node_label": "FAT4",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001291303.... | NM_001291303.3(FAT4):c.14610del (p.Lys4871fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"FAT4\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"FAT4\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_001291303.3(FAT4):c.14610del (p.Lys4871fs)",
"text": "NM_001291303.3(FAT4):c.14610del (p.Lys4871fs) VARIANT_IN_GENE FAT4",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hennekam_lymphangiectasia_lymphedema_syndrome_2",
"... | {"gene": "FAT4", "disease": "Hennekam lymphangiectasia-lymphedema syndrome 2", "pathogenic_variants": ["NM_001291303.3(FAT4):c.13588C>T (p.Gln4530Ter)", "NM_001291303.3(FAT4):c.7204A>C (p.Arg2402=)", "NM_001291303.3(FAT4):c.1195del (p.Leu399fs)", "NM_001291303.3(FAT4):c.7035TGGAAC[3] (p.2346GT[3])", "NM_001291303.3(FAT... | 0.83666 | null |
no_dise_00067 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in REST classified as Pathogenic or Likely Pathogenic for Inborn genetic diseases. | NM_005612.5(REST):c.2515G>T (p.Glu839Ter) VARIANT_IN_GENE REST → NM_005612.5(REST):c.2515G>T (p.Glu839Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inborn genetic diseases | {
"steps": [
{
"hop": 1,
"source_node_id": "REST",
"source_node_type": "GENE",
"source_node_label": "REST",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_005612.5(R... | NM_005612.5(REST):c.2515G>T (p.Glu839Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"REST\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"REST\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_005612.5(REST):c.2515G>T (p.Glu839Ter)",
"text": "NM_005612.5(REST):c.2515G>T (p.Glu839Ter) VARIANT_IN_GENE REST",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inborn_genetic_diseases",
"text": "NM_005612.5(REST):c.2515... | {"gene": "REST", "disease": "Inborn genetic diseases", "pathogenic_variants": ["NM_005612.5(REST):c.2515G>T (p.Glu839Ter)"]} | 0.83666 | null |
no_dise_00171 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in MSH6 classified as Pathogenic or Likely Pathogenic for Hereditary cancer-predisposing syndrome. | NM_000179.3(MSH6):c.3901_3911dup (p.Leu1305fs) VARIANT_IN_GENE MSH6 → NM_000179.3(MSH6):c.3901_3911dup (p.Leu1305fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Hereditary cancer-predisposing syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "MSH6",
"source_node_type": "GENE",
"source_node_label": "MSH6",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000179.3(M... | NM_000179.3(MSH6):c.3901_3911dup (p.Leu1305fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"MSH6\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"MSH6\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_... | [
{
"source_db": "ClinVar",
"source_id": "NM_000179.3(MSH6):c.3901_3911dup (p.Leu1305fs)",
"text": "NM_000179.3(MSH6):c.3901_3911dup (p.Leu1305fs) VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hereditary_cancer_predisposing_syndrome",
"text":... | {"gene": "MSH6", "disease": "Hereditary cancer-predisposing syndrome", "pathogenic_variants": ["NM_000179.3(MSH6):c.2549dup (p.Tyr850Ter)", "NM_000179.3(MSH6):c.3034G>T (p.Glu1012Ter)", "NM_000179.3(MSH6):c.3108dup (p.Phe1037fs)", "NM_000179.3(MSH6):c.2799del (p.Phe933fs)", "NM_000179.3(MSH6):c.3215dup (p.Pro1073fs)", ... | 0.921954 | null |
no_dise_00355 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in PALB2 classified as Pathogenic or Likely Pathogenic for Inherited ovarian cancer (without breast cancer). | NM_024675.4(PALB2):c.2727_2728del (p.Thr911fs) VARIANT_IN_GENE PALB2 → NM_024675.4(PALB2):c.2727_2728del (p.Thr911fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Inherited ovarian cancer (without breast cancer) | {
"steps": [
{
"hop": 1,
"source_node_id": "PALB2",
"source_node_type": "GENE",
"source_node_label": "PALB2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_024675.4... | NM_024675.4(PALB2):c.2727_2728del (p.Thr911fs) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"PALB2\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"PALB2\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brai... | [
{
"source_db": "ClinVar",
"source_id": "NM_024675.4(PALB2):c.2727_2728del (p.Thr911fs)",
"text": "NM_024675.4(PALB2):c.2727_2728del (p.Thr911fs) VARIANT_IN_GENE PALB2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:inherited_ovarian_cancer_without_breast_cancer",
... | {"gene": "PALB2", "disease": "Inherited ovarian cancer (without breast cancer)", "pathogenic_variants": ["NM_024675.4(PALB2):c.2727_2728del (p.Thr911fs)"]} | 0.921954 | null |
no_dise_00530 | disease_reasoning | noncoding_regulatory | medium | 2 | According to ClinVar, name a variant in ATM classified as Pathogenic or Likely Pathogenic for Breast cancer, susceptibility to. | NM_000051.4(ATM):c.3973G>T (p.Glu1325Ter) VARIANT_IN_GENE ATM → NM_000051.4(ATM):c.3973G>T (p.Glu1325Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Breast cancer, susceptibility to | {
"steps": [
{
"hop": 1,
"source_node_id": "ATM",
"source_node_type": "GENE",
"source_node_label": "ATM",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000051.4(ATM... | NM_000051.4(ATM):c.3973G>T (p.Glu1325Ter) | [
"expression"
] | [
"{\"family\": \"transcriptomic\", \"tag\": \"expression\", \"anchor_node_id\": \"ATM\", \"source_db\": \"GTEx\", \"payload\": {\"gene\": \"ATM\", \"tissues\": [\"Adipose_Subcutaneous\", \"Adipose_Visceral_Omentum\", \"Adrenal_Gland\", \"Artery_Aorta\", \"Artery_Coronary\", \"Artery_Tibial\", \"Bladder\", \"Brain_Am... | [
{
"source_db": "ClinVar",
"source_id": "NM_000051.4(ATM):c.3973G>T (p.Glu1325Ter)",
"text": "NM_000051.4(ATM):c.3973G>T (p.Glu1325Ter) VARIANT_IN_GENE ATM",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:breast_cancer_susceptibility_to",
"text": "NM_000051.4(ATM):... | {"gene": "ATM", "disease": "Breast cancer, susceptibility to", "pathogenic_variants": ["NM_000051.4(ATM):c.3973G>T (p.Glu1325Ter)"]} | 0.921954 | null |
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