id string | task_type string | pipeline string | difficulty string | num_hops int64 | question string | context string | reasoning_chain dict | answer string | choices list | modalities list | modality_data list | evidence list | metadata unknown | path_confidence_score float64 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
co_dise_00071 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PSEN1 are classified as Pathogenic or Likely Pathogenic for Mental deterioration? | NM_000021.4(PSEN1):c.314T>G (p.Phe105Cys) VARIANT_IN_GENE PSEN1 -> NM_000021.4(PSEN1):c.314T>G (p.Phe105Cys) VARIANT_HAS_CLINICAL_SIGNIFICANCE Mental deterioration | {
"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.314T>G (p.Phe105Cys) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PSEN1",
"source_db": "UniProt",
"payload": {
"accession": "P49768",
"sequence": "MTELPAPLSYFQNAQMSEDNHLSNTVRSQNDNRERQEHNDRRSLGHPEPLSNGRPQGNSRQVVEQDEEEDEELTLKYGAKHVIMLFVPVTLCMVVVVATIKSVSFYTRKDGQLIYTPFTEDTETVGQRALHSI... | [
{
"source_db": "ClinVar",
"source_id": "NM_000021.4(PSEN1):c.314T>G (p.Phe105Cys)",
"text": "NM_000021.4(PSEN1):c.314T>G (p.Phe105Cys) VARIANT_IN_GENE PSEN1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:mental_deterioration",
"text": "NM_000021.4(PSEN1):c.314T>... | {
"gene": "PSEN1",
"disease": "Mental deterioration",
"pathogenic_variants": [
"NM_000021.4(PSEN1):c.314T>G (p.Phe105Cys)"
]
} | 0.83666 |
co_dise_00072 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KRAS are classified as Pathogenic or Likely Pathogenic for Bladder cancer, transitional cell, somatic? | NM_033360.4(KRAS):c.175G>A (p.Ala59Thr) VARIANT_IN_GENE KRAS -> NM_033360.4(KRAS):c.175G>A (p.Ala59Thr) VARIANT_HAS_CLINICAL_SIGNIFICANCE Bladder cancer, transitional cell, somatic | {
"steps": [
{
"hop": 1,
"source_node_id": "KRAS",
"source_node_type": "GENE",
"source_node_label": "KRAS",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_033360.4(K... | NM_033360.4(KRAS):c.175G>A (p.Ala59Thr) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KRAS",
"source_db": "UniProt",
"payload": {
"accession": "P01116",
"sequence": "MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLA... | [
{
"source_db": "ClinVar",
"source_id": "NM_033360.4(KRAS):c.175G>A (p.Ala59Thr)",
"text": "NM_033360.4(KRAS):c.175G>A (p.Ala59Thr) VARIANT_IN_GENE KRAS",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:bladder_cancer_transitional_cell_somatic",
"text": "NM_033360.4... | {
"gene": "KRAS",
"disease": "Bladder cancer, transitional cell, somatic",
"pathogenic_variants": [
"NM_033360.4(KRAS):c.175G>A (p.Ala59Thr)"
]
} | 0.707107 |
co_dise_00073 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CD274 are classified as Pathogenic or Likely Pathogenic for 9p partial trisomy syndrome? | Single allele VARIANT_IN_GENE CD274 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 9p partial trisomy syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "CD274",
"source_node_type": "GENE",
"source_node_label": "CD274",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD274",
"source_db": "UniProt",
"payload": {
"accession": "Q9NZQ7",
"sequence": "MRIFAVFIFMTYWHLLNAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAP... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CD274",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:9p_partial_trisomy_syndrome",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 9p partial trisomy syndrome... | {
"gene": "CD274",
"disease": "9p partial trisomy syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00074 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BCL11B are classified as Pathogenic or Likely Pathogenic for microcephaly? | NM_138576.4(BCL11B):c.1938_1950del (p.Ala647fs) VARIANT_IN_GENE BCL11B -> NM_138576.4(BCL11B):c.1938_1950del (p.Ala647fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE microcephaly | {
"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.1938_1950del (p.Ala647fs) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BCL11B",
"source_db": "UniProt",
"payload": {
"accession": "Q9C0K0",
"sequence": "MSRRKQGNPQHLSQRELITPEADHVEAAILEEDEGLEIEEPSGLGLMVGGPDPDLLTCGQCQMNFPLGDILVFIEHKRKQCGGSLGACYDKALDKDSPPPSSRSELRKVSEPVEIGIQVTPDEDDHLLSPTK... | [
{
"source_db": "ClinVar",
"source_id": "NM_138576.4(BCL11B):c.1938_1950del (p.Ala647fs)",
"text": "NM_138576.4(BCL11B):c.1938_1950del (p.Ala647fs) VARIANT_IN_GENE BCL11B",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0001149",
"text": "NM_138576.4(BCL11B):c.1938_1... | {
"gene": "BCL11B",
"disease": "microcephaly",
"pathogenic_variants": [
"NM_138576.4(BCL11B):c.1938_1950del (p.Ala647fs)"
]
} | 0.83666 |
co_dise_00075 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in TP53 are classified as Pathogenic or Likely Pathogenic for neurodevelopmental disorder? | Single allele VARIANT_IN_GENE TP53 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE neurodevelopmental disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "TP53",
"source_node_type": "GENE",
"source_node_label": "TP53",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE TP53",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0700092",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE neurodevelopmental disorder",
"confidence": 0.... | {
"gene": "TP53",
"disease": "neurodevelopmental disorder",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00076 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MYC are classified as Pathogenic or Likely Pathogenic for schizophrenia? | Single allele VARIANT_IN_GENE MYC -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia | {
"steps": [
{
"hop": 1,
"source_node_id": "MYC",
"source_node_type": "GENE",
"source_node_label": "MYC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MYC",
"source_db": "UniProt",
"payload": {
"accession": "P01106",
"sequence": "MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MYC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005090",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia",
"confidence": 0.7
}
] | {
"gene": "MYC",
"disease": "schizophrenia",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00077 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in AFDN are classified as Pathogenic or Likely Pathogenic for See cases? | Single allele VARIANT_IN_GENE AFDN -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE See cases | {
"steps": [
{
"hop": 1,
"source_node_id": "AFDN",
"source_node_type": "GENE",
"source_node_label": "AFDN",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | GRCh38/hg38 6q25.3-27(chr6:159915390-170714507)x1; GRCh38/hg38 6q25.3-27(chr6:160359686-170608818)x1; GRCh38/hg38 6q25.3-27(chr6:159825913-170612001)x1; Single allele; GRCh37/hg19 6q26-27(chr6:164276935-170919482)x1 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AFDN",
"source_db": "UniProt",
"payload": {
"accession": "P55196",
"sequence": "MSAGGRDEERRKLADIIHHWNANRLDLFEISQPTEDLEFHGVMRFYFQDKAAGNFATKCIRVSSTATTQDVIETLAEKFRPDMRMLSSPKYSLYEVHVSGERRLDIDEKPLVVQLNWNKDDREGRFVLKNENDA... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE AFDN",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:see_cases",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE See cases",
"confidence": 0.5
}
] | {
"gene": "AFDN",
"disease": "See cases",
"pathogenic_variants": [
"GRCh38/hg38 6q25.3-27(chr6:159915390-170714507)x1",
"GRCh38/hg38 6q25.3-27(chr6:160359686-170608818)x1",
"GRCh38/hg38 6q25.3-27(chr6:159825913-170612001)x1",
"Single allele",
"GRCh37/hg19 6q26-27(chr6:164276935-170919482)x1",
... | 0.707107 |
co_dise_00078 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACTB are classified as Pathogenic or Likely Pathogenic for not specified? | GRCh37/hg19 7p22.2-22.1(chr7:4099939-5760730)x3 VARIANT_IN_GENE ACTB -> GRCh37/hg19 7p22.2-22.1(chr7:4099939-5760730)x3 VARIANT_HAS_CLINICAL_SIGNIFICANCE not specified | {
"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 7p22.2-22.1(chr7:4099939-5760730)x3; GRCh37/hg19 7p22.1(chr7:5052768-5999452)x3; GRCh37/hg19 7p22.1(chr7:5413143-5948815)x3; GRCh37/hg19 7p22.1(chr7:5376510-5934779)x3 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACTB",
"source_db": "UniProt",
"payload": {
"accession": "P60709",
"sequence": "MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYV... | [
{
"source_db": "ClinVar",
"source_id": "GRCh37/hg19 7p22.2-22.1(chr7:4099939-5760730)x3",
"text": "GRCh37/hg19 7p22.2-22.1(chr7:4099939-5760730)x3 VARIANT_IN_GENE ACTB",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:not_specified",
"text": "GRCh37/hg19 7p22.2-22.... | {
"gene": "ACTB",
"disease": "not specified",
"pathogenic_variants": [
"GRCh37/hg19 7p22.2-22.1(chr7:4099939-5760730)x3",
"GRCh37/hg19 7p22.1(chr7:5052768-5999452)x3",
"GRCh37/hg19 7p22.1(chr7:5413143-5948815)x3",
"GRCh37/hg19 7p22.1(chr7:5376510-5934779)x3"
]
} | 0.83666 |
co_dise_00079 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BRCA1 are classified as Pathogenic or Likely Pathogenic for breast neoplasm? | NM_007294.4(BRCA1):c.192T>G (p.Cys64Trp) VARIANT_IN_GENE BRCA1 -> NM_007294.4(BRCA1):c.192T>G (p.Cys64Trp) VARIANT_HAS_CLINICAL_SIGNIFICANCE breast neoplasm | {
"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.192T>G (p.Cys64Trp) | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "ClinVar",
"source_id": "NM_007294.4(BRCA1):c.192T>G (p.Cys64Trp)",
"text": "NM_007294.4(BRCA1):c.192T>G (p.Cys64Trp) VARIANT_IN_GENE BRCA1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0021100",
"text": "NM_007294.4(BRCA1):c.192T>G (p.Cys64Trp) VA... | {
"gene": "BRCA1",
"disease": "breast neoplasm",
"pathogenic_variants": [
"NM_007294.4(BRCA1):c.192T>G (p.Cys64Trp)"
]
} | 0.921954 |
co_dise_00080 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH6 are classified as Pathogenic or Likely Pathogenic for Kleefstra syndrome 2? | Single allele VARIANT_IN_GENE MSH6 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Kleefstra syndrome 2 | {
"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": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0054701",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Kleefstra syndrome 2",
"confidence": 0.7
}
] | {
"gene": "MSH6",
"disease": "Kleefstra syndrome 2",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00081 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BRCA1 are classified as Pathogenic or Likely Pathogenic for polydactyly? | Single allele VARIANT_IN_GENE BRCA1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE polydactyly | {
"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": "Single alle... | Single allele | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE BRCA1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0021003",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE polydactyly",
"confidence": 0.5
}
] | {
"gene": "BRCA1",
"disease": "polydactyly",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00082 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BRCA2 are classified as Pathogenic or Likely Pathogenic for breast cancer? | NM_000059.4(BRCA2):c.7008-1_7435+372del VARIANT_IN_GENE BRCA2 -> NM_000059.4(BRCA2):c.7008-1_7435+372del VARIANT_HAS_CLINICAL_SIGNIFICANCE breast cancer | {
"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.3085dup (p.Met1029fs); NM_000059.4(BRCA2):c.7008-1_7435+372del; NM_000059.4(BRCA2):c.6819delinsGT (p.Gly2274fs) | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA2",
"source_db": "UniProt",
"payload": {
"accession": "P51587",
"sequence": "MPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPYNSEPAEESEHKNNNYEPNLFKTPQRKPSYNQLASTPIIFKEQGLTLPLYQSPVKELDKFKLDLGRNVPNSRHKSLRTVKTKMDQADDVSCP... | [
{
"source_db": "ClinVar",
"source_id": "NM_000059.4(BRCA2):c.7008-1_7435+372del",
"text": "NM_000059.4(BRCA2):c.7008-1_7435+372del VARIANT_IN_GENE BRCA2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0007254",
"text": "NM_000059.4(BRCA2):c.7008-1_7435+372del VARIA... | {
"gene": "BRCA2",
"disease": "breast cancer",
"pathogenic_variants": [
"NM_000059.4(BRCA2):c.3085dup (p.Met1029fs)",
"NM_000059.4(BRCA2):c.7008-1_7435+372del",
"NM_000059.4(BRCA2):c.6819delinsGT (p.Gly2274fs)"
]
} | 0.707107 |
co_dise_00083 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in APP are classified as Pathogenic or Likely Pathogenic for syndromic X-linked intellectual disability Lubs type? | Single allele VARIANT_IN_GENE APP -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE syndromic X-linked intellectual disability Lubs type | {
"steps": [
{
"hop": 1,
"source_node_id": "APP",
"source_node_type": "GENE",
"source_node_label": "APP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APP",
"source_db": "UniProt",
"payload": {
"accession": "P05067",
"sequence": "MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE APP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0010283",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE syndromic X-linked intellectual disability Lubs typ... | {
"gene": "APP",
"disease": "syndromic X-linked intellectual disability Lubs type",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00084 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ABL1 are classified as Pathogenic or Likely Pathogenic for Kabuki syndrome 1? | Single allele VARIANT_IN_GENE ABL1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Kabuki syndrome 1 | {
"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": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL1",
"source_db": "UniProt",
"payload": {
"accession": "P00519",
"sequence": "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSR... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ABL1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0007843",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Kabuki syndrome 1",
"confidence": 0.7
}
] | {
"gene": "ABL1",
"disease": "Kabuki syndrome 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00085 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACVR1 are classified as Pathogenic or Likely Pathogenic for schizophrenia? | Single allele VARIANT_IN_GENE ACVR1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia | {
"steps": [
{
"hop": 1,
"source_node_id": "ACVR1",
"source_node_type": "GENE",
"source_node_label": "ACVR1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACVR1",
"source_db": "UniProt",
"payload": {
"accession": "Q04771",
"sequence": "MVDGVMILPVLIMIALPSPSMEDEKPKVNPKLYMCVCEGLSCGNEDHCEGQQCFSSLSINDGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLPTKGKSFPGTQNFHLEVGLIILSVVF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ACVR1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005090",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE schizophrenia",
"confidence": 0.7
}
] | {
"gene": "ACVR1",
"disease": "schizophrenia",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00086 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CTNNB1 are classified as Pathogenic or Likely Pathogenic for urinary bladder cancer? | NM_001904.4(CTNNB1):c.100G>A (p.Gly34Arg) VARIANT_IN_GENE CTNNB1 -> NM_001904.4(CTNNB1):c.100G>A (p.Gly34Arg) VARIANT_HAS_CLINICAL_SIGNIFICANCE urinary bladder cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "CTNNB1",
"source_node_type": "GENE",
"source_node_label": "CTNNB1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001904... | NM_001904.4(CTNNB1):c.100G>A (p.Gly34Arg); NM_001904.4(CTNNB1):c.98C>T (p.Ser33Phe) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CTNNB1",
"source_db": "UniProt",
"payload": {
"accession": "P35222",
"sequence": "MATQADLMELDMAMEPDRKAAVSHWQQQSYLDSGIHSGATTTAPSLSGKGNPEEEDVDTSQVLYEWEQGFSQSFTQEQVADIDGQYAMTRAQRVRAAMFPETLDEGMQIPSTQFDAAHPTNVQRLAEPSQML... | [
{
"source_db": "ClinVar",
"source_id": "NM_001904.4(CTNNB1):c.100G>A (p.Gly34Arg)",
"text": "NM_001904.4(CTNNB1):c.100G>A (p.Gly34Arg) VARIANT_IN_GENE CTNNB1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0001187",
"text": "NM_001904.4(CTNNB1):c.100G>A (p.Gly34Arg... | {
"gene": "CTNNB1",
"disease": "urinary bladder cancer",
"pathogenic_variants": [
"NM_001904.4(CTNNB1):c.100G>A (p.Gly34Arg)",
"NM_001904.4(CTNNB1):c.98C>T (p.Ser33Phe)"
]
} | 0.707107 |
co_dise_00087 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MET are classified as Pathogenic or Likely Pathogenic for pediatric hepatocellular carcinoma? | NM_000245.4(MET):c.3750G>A (p.Met1250Ile) VARIANT_IN_GENE MET -> NM_000245.4(MET):c.3750G>A (p.Met1250Ile) VARIANT_HAS_CLINICAL_SIGNIFICANCE pediatric hepatocellular carcinoma | {
"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.3731A>G (p.Lys1244Arg); NM_000245.4(MET):c.3750G>A (p.Met1250Ile) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MET",
"source_db": "UniProt",
"payload": {
"accession": "P08581",
"sequence": "MKAPAVLAPGILVLLFTLVQRSNGECKEALAKSEMNVNMKYQLPNFTAETPIQNVILHEHHIFLGATNYIYVLNEEDLQKVAEYKTGPVLEHPDCFPCQDCSSKANLSGGVWKDNINMALVVDTYYDDQLISCGS... | [
{
"source_db": "ClinVar",
"source_id": "NM_000245.4(MET):c.3750G>A (p.Met1250Ile)",
"text": "NM_000245.4(MET):c.3750G>A (p.Met1250Ile) VARIANT_IN_GENE MET",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0018055",
"text": "NM_000245.4(MET):c.3750G>A (p.Met1250Ile) V... | {
"gene": "MET",
"disease": "pediatric hepatocellular carcinoma",
"pathogenic_variants": [
"NM_000245.4(MET):c.3731A>G (p.Lys1244Arg)",
"NM_000245.4(MET):c.3750G>A (p.Met1250Ile)"
]
} | 0.707107 |
co_dise_00088 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BARD1 are classified as Pathogenic or Likely Pathogenic for tricho-dento-osseous syndrome? | Single allele VARIANT_IN_GENE BARD1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE tricho-dento-osseous syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "BARD1",
"source_node_type": "GENE",
"source_node_label": "BARD1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE BARD1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0008592",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE tricho-dento-osseous syndrome",
"confidence":... | {
"gene": "BARD1",
"disease": "tricho-dento-osseous syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00089 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BARD1 are classified as Pathogenic or Likely Pathogenic for distal 10q deletion syndrome? | Single allele VARIANT_IN_GENE BARD1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE distal 10q deletion syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "BARD1",
"source_node_type": "GENE",
"source_node_label": "BARD1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE BARD1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0012315",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE distal 10q deletion syndrome",
"confidence": ... | {
"gene": "BARD1",
"disease": "distal 10q deletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00090 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CHCHD10 are classified as Pathogenic or Likely Pathogenic for developmental and epileptic encephalopathy, 54? | Single allele VARIANT_IN_GENE CHCHD10 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE developmental and epileptic encephalopathy, 54 | {
"steps": [
{
"hop": 1,
"source_node_id": "CHCHD10",
"source_node_type": "GENE",
"source_node_label": "CHCHD10",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single ... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHCHD10",
"source_db": "UniProt",
"payload": {
"accession": "Q8WYQ3",
"sequence": "MPRGSRSAASRPASRPAAPSAHPPAHPPPSAAAPAPAPSGQPGLMAQMATTAAGVAVGSAVGHVMGSALTGAFSGGSSEPSQPAVQQAPTPAAPQPLQMGPCAYEIRQFLDCSTTQSDLSLCEGFSEALKQ... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CHCHD10",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0033363",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE developmental and epileptic encephalopathy, 54"... | {
"gene": "CHCHD10",
"disease": "developmental and epileptic encephalopathy, 54",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00091 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ABL1 are classified as Pathogenic or Likely Pathogenic for Severe global developmental delay? | Single allele VARIANT_IN_GENE ABL1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Severe global developmental delay | {
"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": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ABL1",
"source_db": "UniProt",
"payload": {
"accession": "P00519",
"sequence": "MLEICLKLVGCKSKKGLSSSSSCYLEEALQRPVASDFEPQGLSEAARWNSKENLLAGPSENDPNLFVALYDFVASGDNTLSITKGEKLRVLGYNHNGEWCEAQTKNGQGWVPSNYITPVNSLEKHSWYHGPVSR... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ABL1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:severe_global_developmental_delay",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Severe global developm... | {
"gene": "ABL1",
"disease": "Severe global developmental delay",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00092 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH6 are classified as Pathogenic or Likely Pathogenic for hereditary breast carcinoma? | NM_000179.3(MSH6):c.408_418del (p.Asp136fs) VARIANT_IN_GENE MSH6 -> NM_000179.3(MSH6):c.408_418del (p.Asp136fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE hereditary breast carcinoma | {
"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.408_418del (p.Asp136fs); NM_000179.3(MSH6):c.312del (p.Trp105fs); NM_000179.3(MSH6):c.*15A>C; Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "NM_000179.3(MSH6):c.408_418del (p.Asp136fs)",
"text": "NM_000179.3(MSH6):c.408_418del (p.Asp136fs) VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0016419",
"text": "NM_000179.3(MSH6):c.408_418del (p.Asp1... | {
"gene": "MSH6",
"disease": "hereditary breast carcinoma",
"pathogenic_variants": [
"NM_000179.3(MSH6):c.408_418del (p.Asp136fs)",
"NM_000179.3(MSH6):c.312del (p.Trp105fs)",
"NM_000179.3(MSH6):c.*15A>C",
"Single allele"
]
} | 0.83666 |
co_dise_00093 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2C are classified as Pathogenic or Likely Pathogenic for hereditary breast carcinoma? | Single allele VARIANT_IN_GENE KMT2C -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE hereditary breast carcinoma | {
"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": "Single alle... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2C",
"source_db": "UniProt",
"payload": {
"accession": "Q8NEZ4",
"sequence": "MSSEEDKSVEQPQPPPPPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGKTAVEDEDSMDGLETTETETIVETEIKEQSAEEDAEAEVDNSKQLIPTLQRSVSEESANSLVSVGVEAKISEQL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE KMT2C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0016419",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE hereditary breast carcinoma",
"confidence": 0... | {
"gene": "KMT2C",
"disease": "hereditary breast carcinoma",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00094 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BRCA2 are classified as Pathogenic or Likely Pathogenic for pancreatic cancer, susceptibility to, 2? | NM_000059.4(BRCA2):c.4234_4236delinsC (p.Thr1412fs) VARIANT_IN_GENE BRCA2 -> NM_000059.4(BRCA2):c.4234_4236delinsC (p.Thr1412fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE pancreatic cancer, 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.4234_4236delinsC (p.Thr1412fs) | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA2",
"source_db": "UniProt",
"payload": {
"accession": "P51587",
"sequence": "MPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPYNSEPAEESEHKNNNYEPNLFKTPQRKPSYNQLASTPIIFKEQGLTLPLYQSPVKELDKFKLDLGRNVPNSRHKSLRTVKTKMDQADDVSCP... | [
{
"source_db": "ClinVar",
"source_id": "NM_000059.4(BRCA2):c.4234_4236delinsC (p.Thr1412fs)",
"text": "NM_000059.4(BRCA2):c.4234_4236delinsC (p.Thr1412fs) VARIANT_IN_GENE BRCA2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013235",
"text": "NM_000059.4(BRCA2):c.... | {
"gene": "BRCA2",
"disease": "pancreatic cancer, susceptibility to, 2",
"pathogenic_variants": [
"NM_000059.4(BRCA2):c.4234_4236delinsC (p.Thr1412fs)"
]
} | 0.83666 |
co_dise_00095 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CDKN2A are classified as Pathogenic or Likely Pathogenic for melanoma-pancreatic cancer syndrome? | NM_000077.5(CDKN2A):c.165C>T (p.Gly55=) VARIANT_IN_GENE CDKN2A -> NM_000077.5(CDKN2A):c.165C>T (p.Gly55=) VARIANT_HAS_CLINICAL_SIGNIFICANCE melanoma-pancreatic cancer 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.73del (p.Arg24_Val25insTer); NM_000077.5(CDKN2A):c.68dup (p.Arg24fs); NM_000077.5(CDKN2A):c.18del (p.Ser7fs); NM_058195.4(CDKN2A):c.26_27dup (p.Arg10fs); NM_058195.4(CDKN2A):c.169C>T (p.Gln57Ter) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDKN2A",
"source_db": "UniProt",
"payload": {
"accession": "Q8N726",
"sequence": "MVRRFLVTLRIRRACGPPRVRVFVVHIPRLTGEWAAPGAPAAVALVLMLLRSQRLGQQPLPRRPGHDDGQRPSGGAAAAPRRGAQLRRPRHSHPTRARRCPGGLPGHAGGAAPGRGAAGRARCLGPSARGPG... | [
{
"source_db": "ClinVar",
"source_id": "NM_000077.5(CDKN2A):c.165C>T (p.Gly55=)",
"text": "NM_000077.5(CDKN2A):c.165C>T (p.Gly55=) VARIANT_IN_GENE CDKN2A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0011713",
"text": "NM_000077.5(CDKN2A):c.165C>T (p.Gly55=) VARI... | {
"gene": "CDKN2A",
"disease": "melanoma-pancreatic cancer syndrome",
"pathogenic_variants": [
"NM_000077.5(CDKN2A):c.73del (p.Arg24_Val25insTer)",
"NM_000077.5(CDKN2A):c.68dup (p.Arg24fs)",
"NM_000077.5(CDKN2A):c.18del (p.Ser7fs)",
"NM_058195.4(CDKN2A):c.26_27dup (p.Arg10fs)",
"NM_058195.4(CD... | 0.83666 |
co_dise_00096 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PIK3CA are classified as Pathogenic or Likely Pathogenic for overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes? | NM_006218.4(PIK3CA):c.3140A>G (p.His1047Arg) VARIANT_IN_GENE PIK3CA -> NM_006218.4(PIK3CA):c.3140A>G (p.His1047Arg) VARIANT_HAS_CLINICAL_SIGNIFICANCE overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes | {
"steps": [
{
"hop": 1,
"source_node_id": "PIK3CA",
"source_node_type": "GENE",
"source_node_label": "PIK3CA",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_006218... | NM_006218.4(PIK3CA):c.2176G>A (p.Glu726Lys); NM_006218.4(PIK3CA):c.2740G>A (p.Gly914Arg); NM_006218.4(PIK3CA):c.1624G>A (p.Glu542Lys); NM_006218.4(PIK3CA):c.3140A>G (p.His1047Arg); NM_006218.4(PIK3CA):c.325GAA[1] (p.Glu110del) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PIK3CA",
"source_db": "UniProt",
"payload": {
"accession": "P42336",
"sequence": "MPPRPSSGELWGIHLMPPRILVECLLPNGMIVTLECLREATLITIKHELFKEARKYPLHQLLQDESSYIFVSVTQEAEREEFFDETRRLCDLRLFQPFLKVIEPVGNREEKILNREIGFAIGMPVCEFDMVK... | [
{
"source_db": "ClinVar",
"source_id": "NM_006218.4(PIK3CA):c.3140A>G (p.His1047Arg)",
"text": "NM_006218.4(PIK3CA):c.3140A>G (p.His1047Arg) VARIANT_IN_GENE PIK3CA",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0100283",
"text": "NM_006218.4(PIK3CA):c.3140A>G (p.H... | {
"gene": "PIK3CA",
"disease": "overgrowth syndrome and/or cerebral malformations due to abnormalities in MTOR pathway genes",
"pathogenic_variants": [
"NM_006218.4(PIK3CA):c.2176G>A (p.Glu726Lys)",
"NM_006218.4(PIK3CA):c.2740G>A (p.Gly914Arg)",
"NM_006218.4(PIK3CA):c.1624G>A (p.Glu542Lys)",
"NM_0... | 0.974679 |
co_dise_00097 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NOTCH1 are classified as Pathogenic or Likely Pathogenic for Lynch syndrome? | Single allele VARIANT_IN_GENE NOTCH1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Lynch syndrome | {
"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": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005835",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Lynch syndrome",
"confidence": 0.7
}
] | {
"gene": "NOTCH1",
"disease": "Lynch syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00098 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in TP53 are classified as Pathogenic or Likely Pathogenic for Rubinstein-Taybi syndrome due to CREBBP mutations? | Single allele VARIANT_IN_GENE TP53 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Rubinstein-Taybi syndrome due to CREBBP mutations | {
"steps": [
{
"hop": 1,
"source_node_id": "TP53",
"source_node_type": "GENE",
"source_node_label": "TP53",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TP53",
"source_db": "UniProt",
"payload": {
"accession": "P04637",
"sequence": "MEEPQSDPSVEPPLSQETFSDLWKLLPENNVLSPLPSQAMDDLMLSPDDIEQWFTEDPGPDEAPRMPEAAPPVAPAPAAPTPAAPAPAPSWPLSSSVPSQKTYQGSYGFRLGFLHSGTAKSVTCTYSPALNKMF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE TP53",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0008393",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Rubinstein-Taybi syndrome due to CREBBP mutations"... | {
"gene": "TP53",
"disease": "Rubinstein-Taybi syndrome due to CREBBP mutations",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00099 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ASXL1 are classified as Pathogenic or Likely Pathogenic for myelodysplastic syndrome? | NM_015338.6(ASXL1):c.2068_2069del (p.Asp690fs) VARIANT_IN_GENE ASXL1 -> NM_015338.6(ASXL1):c.2068_2069del (p.Asp690fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE myelodysplastic syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "ASXL1",
"source_node_type": "GENE",
"source_node_label": "ASXL1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_015338.6... | NM_015338.6(ASXL1):c.2100T>A (p.Tyr700Ter); NM_015338.6(ASXL1):c.4127dup (p.Pro1377fs); NM_015338.6(ASXL1):c.3747_3748del (p.Met1249fs); NM_015338.6(ASXL1):c.2068_2069del (p.Asp690fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ASXL1",
"source_db": "UniProt",
"payload": {
"accession": "Q8IXJ9",
"sequence": "MKDKQKKKKERTWAEAARLVLENYSDAPMTPKQILQVIEAEGLKEMRSGTSPLACLNAMLHSNSRGGEGLFYKLPGRISLFTLKKDALQWSRHPATVEGEEPEDTADVESCGSNEASTVSGENDVSLDETSSN... | [
{
"source_db": "ClinVar",
"source_id": "NM_015338.6(ASXL1):c.2068_2069del (p.Asp690fs)",
"text": "NM_015338.6(ASXL1):c.2068_2069del (p.Asp690fs) VARIANT_IN_GENE ASXL1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0018881",
"text": "NM_015338.6(ASXL1):c.2068_2069d... | {
"gene": "ASXL1",
"disease": "myelodysplastic syndrome",
"pathogenic_variants": [
"NM_015338.6(ASXL1):c.2100T>A (p.Tyr700Ter)",
"NM_015338.6(ASXL1):c.4127dup (p.Pro1377fs)",
"NM_015338.6(ASXL1):c.3747_3748del (p.Met1249fs)",
"NM_015338.6(ASXL1):c.2068_2069del (p.Asp690fs)"
]
} | 0.83666 |
co_dise_00100 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in RAD51C are classified as Pathogenic or Likely Pathogenic for hereditary breast ovarian cancer syndrome? | NC_000017.10:g.(56801462_56809844)_(56809906_56811478)del VARIANT_IN_GENE RAD51C -> NC_000017.10:g.(56801462_56809844)_(56809906_56811478)del VARIANT_HAS_CLINICAL_SIGNIFICANCE hereditary breast ovarian cancer syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "RAD51C",
"source_node_type": "GENE",
"source_node_label": "RAD51C",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NC_000017... | NC_000017.10:g.(56774221_56780556)_(56812973_?)del; NC_000017.10:g.(?_56780557)_(56780690_?)del; NC_000017.10:g.(56787352_56798106)_(56812973_?)del; NC_000017.10:g.(56780691_56787219)_(56812973_?)del; NC_000017.10:g.(56801462_56809844)_(56809906_56811478)del | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RAD51C",
"source_db": "UniProt",
"payload": {
"accession": "O43502",
"sequence": "MRGKTFRFEMQRDLVSFPLSPAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKAEALETLQIIRRECLTNKPRYAGTSESHKKCTALELLEQEHTQGFIITFCSALDDILGGGVPLMKTTEICGAPGVGKT... | [
{
"source_db": "ClinVar",
"source_id": "NC_000017.10:g.(56801462_56809844)_(56809906_56811478)del",
"text": "NC_000017.10:g.(56801462_56809844)_(56809906_56811478)del VARIANT_IN_GENE RAD51C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0003582",
"text": "NC_00001... | {
"gene": "RAD51C",
"disease": "hereditary breast ovarian cancer syndrome",
"pathogenic_variants": [
"NC_000017.10:g.(56774221_56780556)_(56812973_?)del",
"NC_000017.10:g.(?_56780557)_(56780690_?)del",
"NC_000017.10:g.(56787352_56798106)_(56812973_?)del",
"NC_000017.10:g.(56780691_56787219)_(56812... | 0.83666 |
co_dise_00101 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NLRP3 are classified as Pathogenic or Likely Pathogenic for Familial amyloid nephropathy with urticaria AND deafness? | NM_001243133.2(NLRP3):c.2575T>C (p.Tyr859His) VARIANT_IN_GENE NLRP3 -> NM_001243133.2(NLRP3):c.2575T>C (p.Tyr859His) VARIANT_HAS_CLINICAL_SIGNIFICANCE Familial amyloid nephropathy with urticaria AND deafness | {
"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.2575T>C (p.Tyr859His); NM_001243133.2(NLRP3):c.1712T>G (p.Leu571Trp); NM_001243133.2(NLRP3):c.1985T>C (p.Met662Thr); NM_001243133.2(NLRP3):c.1705G>C (p.Gly569Arg) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NLRP3",
"source_db": "UniProt",
"payload": {
"accession": "Q96P20",
"sequence": "MKMASTRCKLARYLEDLEDVDLKKFKMHLEDYPPQKGCIPLPRGQTEKADHVDLATLMIDFNGEEKAWAMAVWIFAAINRRDLYEKAKRDEPKWGSDNARVSNPTVICQEDSIEEEWMGLLEYLSRISICKMK... | [
{
"source_db": "ClinVar",
"source_id": "NM_001243133.2(NLRP3):c.2575T>C (p.Tyr859His)",
"text": "NM_001243133.2(NLRP3):c.2575T>C (p.Tyr859His) VARIANT_IN_GENE NLRP3",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:familial_amyloid_nephropathy_with_urticaria_and_deafne... | {
"gene": "NLRP3",
"disease": "Familial amyloid nephropathy with urticaria AND deafness",
"pathogenic_variants": [
"NM_001243133.2(NLRP3):c.2575T>C (p.Tyr859His)",
"NM_001243133.2(NLRP3):c.1712T>G (p.Leu571Trp)",
"NM_001243133.2(NLRP3):c.1985T>C (p.Met662Thr)",
"NM_001243133.2(NLRP3):c.1705G>C (p.... | 0.921954 |
co_dise_00102 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ADRA2B are classified as Pathogenic or Likely Pathogenic for T-cell acute lymphoblastic leukemia? | Single allele VARIANT_IN_GENE ADRA2B -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE T-cell acute lymphoblastic leukemia | {
"steps": [
{
"hop": 1,
"source_node_id": "ADRA2B",
"source_node_type": "GENE",
"source_node_label": "ADRA2B",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADRA2B",
"source_db": "UniProt",
"payload": {
"accession": "P18089",
"sequence": "MDHQDPYSVQATAAIAAAITFLILFTIFGNALVILAVLTSRSLRAPQNLFLVSLAAADILVATLIIPFSLANELLGYWYFRRTWCEVYLALDVLFCTSSIVHLCAISLDRYWAVSRALEYNSKRTPRRIKCI... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ADRA2B",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0004963",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE T-cell acute lymphoblastic leukemia",
"confi... | {
"gene": "ADRA2B",
"disease": "T-cell acute lymphoblastic leukemia",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00103 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ASXL1 are classified as Pathogenic or Likely Pathogenic for Bohring-Opitz syndrome? | NM_015338.6(ASXL1):c.2461dup (p.Asp821fs) VARIANT_IN_GENE ASXL1 -> NM_015338.6(ASXL1):c.2461dup (p.Asp821fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE Bohring-Opitz syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "ASXL1",
"source_node_type": "GENE",
"source_node_label": "ASXL1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_015338.6... | NM_015338.6(ASXL1):c.1636C>T (p.Gln546Ter); NM_015338.6(ASXL1):c.1091del (p.Gly364fs); NM_015338.6(ASXL1):c.374-1G>A; NM_015338.6(ASXL1):c.472-2A>G; NM_015338.6(ASXL1):c.2982del (p.His995fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ASXL1",
"source_db": "UniProt",
"payload": {
"accession": "Q8IXJ9",
"sequence": "MKDKQKKKKERTWAEAARLVLENYSDAPMTPKQILQVIEAEGLKEMRSGTSPLACLNAMLHSNSRGGEGLFYKLPGRISLFTLKKDALQWSRHPATVEGEEPEDTADVESCGSNEASTVSGENDVSLDETSSN... | [
{
"source_db": "ClinVar",
"source_id": "NM_015338.6(ASXL1):c.2461dup (p.Asp821fs)",
"text": "NM_015338.6(ASXL1):c.2461dup (p.Asp821fs) VARIANT_IN_GENE ASXL1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0011510",
"text": "NM_015338.6(ASXL1):c.2461dup (p.Asp821fs)... | {
"gene": "ASXL1",
"disease": "Bohring-Opitz syndrome",
"pathogenic_variants": [
"NM_015338.6(ASXL1):c.1636C>T (p.Gln546Ter)",
"NM_015338.6(ASXL1):c.1091del (p.Gly364fs)",
"NM_015338.6(ASXL1):c.374-1G>A",
"NM_015338.6(ASXL1):c.472-2A>G",
"NM_015338.6(ASXL1):c.2982del (p.His995fs)",
"NM_015... | 0.83666 |
co_dise_00104 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in LEPR are classified as Pathogenic or Likely Pathogenic for autism spectrum disorder? | Single allele VARIANT_IN_GENE LEPR -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE autism spectrum disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "LEPR",
"source_node_type": "GENE",
"source_node_label": "LEPR",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "LEPR",
"source_db": "UniProt",
"payload": {
"accession": "P48357",
"sequence": "MICQKFCVVLLHWEFIYVITAFNLSYPITPWRFKLSCMPPNSTYDYFLLPAGLSKNTSNSNGHYETAVEPKFNSSGTHFSNLSKTTFHCCFRSEQDRNCSLCADNIEGKTFVSTVNSLVFQQIDANWNIQCWLK... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE LEPR",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005258",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE autism spectrum disorder",
"confidence": 0.7
... | {
"gene": "LEPR",
"disease": "autism spectrum disorder",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00105 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACKR3 are classified as Pathogenic or Likely Pathogenic for 4p partial monosomy syndrome? | Single allele VARIANT_IN_GENE ACKR3 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 4p partial monosomy syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "ACKR3",
"source_node_type": "GENE",
"source_node_label": "ACKR3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACKR3",
"source_db": "UniProt",
"payload": {
"accession": "P25106",
"sequence": "MDLHLFDYSEPGNFSDISWPCNSSDCIVVDTVMCPNMPNKSVLLYTLSFIYIFIFVIGMIANSVVVWVNIQAKTTGYDTHCYILNLAIADLWVVLTIPVWVVSLVQHNQWPMGELTCKVTHLIFSINLFGSIF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ACKR3",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:4p_partial_monosomy_syndrome",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 4p partial monosomy syndro... | {
"gene": "ACKR3",
"disease": "4p partial monosomy syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00106 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CDKN2A are classified as Pathogenic or Likely Pathogenic for Kleefstra syndrome 2? | Single allele VARIANT_IN_GENE CDKN2A -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Kleefstra syndrome 2 | {
"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": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDKN2A",
"source_db": "UniProt",
"payload": {
"accession": "Q8N726",
"sequence": "MVRRFLVTLRIRRACGPPRVRVFVVHIPRLTGEWAAPGAPAAVALVLMLLRSQRLGQQPLPRRPGHDDGQRPSGGAAAAPRRGAQLRRPRHSHPTRARRCPGGLPGHAGGAAPGRGAAGRARCLGPSARGPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CDKN2A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0054701",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Kleefstra syndrome 2",
"confidence": 0.7
}... | {
"gene": "CDKN2A",
"disease": "Kleefstra syndrome 2",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00107 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CHEK2 are classified as Pathogenic or Likely Pathogenic for CHEK2-related disorder? | NM_007194.4(CHEK2):c.433C>T (p.Arg145Trp) VARIANT_IN_GENE CHEK2 -> NM_007194.4(CHEK2):c.433C>T (p.Arg145Trp) VARIANT_HAS_CLINICAL_SIGNIFICANCE CHEK2-related disorder | {
"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.349A>G (p.Arg117Gly); NM_007194.4(CHEK2):c.433C>T (p.Arg145Trp) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "NM_007194.4(CHEK2):c.433C>T (p.Arg145Trp)",
"text": "NM_007194.4(CHEK2):c.433C>T (p.Arg145Trp) VARIANT_IN_GENE CHEK2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:chek2_related_disorder",
"text": "NM_007194.4(CHEK2):c.433... | {
"gene": "CHEK2",
"disease": "CHEK2-related disorder",
"pathogenic_variants": [
"NM_007194.4(CHEK2):c.349A>G (p.Arg117Gly)",
"NM_007194.4(CHEK2):c.433C>T (p.Arg145Trp)"
]
} | 0.921954 |
co_dise_00108 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ADRA2B are classified as Pathogenic or Likely Pathogenic for chromosome 4q21 deletion syndrome? | Single allele VARIANT_IN_GENE ADRA2B -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE chromosome 4q21 deletion syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "ADRA2B",
"source_node_type": "GENE",
"source_node_label": "ADRA2B",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADRA2B",
"source_db": "UniProt",
"payload": {
"accession": "P18089",
"sequence": "MDHQDPYSVQATAAIAAAITFLILFTIFGNALVILAVLTSRSLRAPQNLFLVSLAAADILVATLIIPFSLANELLGYWYFRRTWCEVYLALDVLFCTSSIVHLCAISLDRYWAVSRALEYNSKRTPRRIKCI... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ADRA2B",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013292",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE chromosome 4q21 deletion syndrome",
"confide... | {
"gene": "ADRA2B",
"disease": "chromosome 4q21 deletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00109 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2C are classified as Pathogenic or Likely Pathogenic for chromosome 4q21 deletion syndrome? | Single allele VARIANT_IN_GENE KMT2C -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE chromosome 4q21 deletion syndrome | {
"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": "Single alle... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2C",
"source_db": "UniProt",
"payload": {
"accession": "Q8NEZ4",
"sequence": "MSSEEDKSVEQPQPPPPPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGKTAVEDEDSMDGLETTETETIVETEIKEQSAEEDAEAEVDNSKQLIPTLQRSVSEESANSLVSVGVEAKISEQL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE KMT2C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013292",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE chromosome 4q21 deletion syndrome",
"confiden... | {
"gene": "KMT2C",
"disease": "chromosome 4q21 deletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00110 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CHCHD10 are classified as Pathogenic or Likely Pathogenic for intellectual disability? | Single allele VARIANT_IN_GENE CHCHD10 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE intellectual disability | {
"steps": [
{
"hop": 1,
"source_node_id": "CHCHD10",
"source_node_type": "GENE",
"source_node_label": "CHCHD10",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single ... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHCHD10",
"source_db": "UniProt",
"payload": {
"accession": "Q8WYQ3",
"sequence": "MPRGSRSAASRPASRPAAPSAHPPAHPPPSAAAPAPAPSGQPGLMAQMATTAAGVAVGSAVGHVMGSALTGAFSGGSSEPSQPAVQQAPTPAAPQPLQMGPCAYEIRQFLDCSTTQSDLSLCEGFSEALKQ... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CHCHD10",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0001071",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE intellectual disability",
"confidence": 0.7... | {
"gene": "CHCHD10",
"disease": "intellectual disability",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00111 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BARD1 are classified as Pathogenic or Likely Pathogenic for Deletion of long arm of chromosome 18? | Single allele VARIANT_IN_GENE BARD1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Deletion of long arm of chromosome 18 | {
"steps": [
{
"hop": 1,
"source_node_id": "BARD1",
"source_node_type": "GENE",
"source_node_label": "BARD1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE BARD1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:deletion_of_long_arm_of_chromosome_18",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Deletion of long ... | {
"gene": "BARD1",
"disease": "Deletion of long arm of chromosome 18",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00112 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ERBB4 are classified as Pathogenic or Likely Pathogenic for NK-cell enteropathy? | NM_005235.3(ERBB4):c.785G>A (p.Cys262Tyr) VARIANT_IN_GENE ERBB4 -> NM_005235.3(ERBB4):c.785G>A (p.Cys262Tyr) VARIANT_HAS_CLINICAL_SIGNIFICANCE NK-cell enteropathy | {
"steps": [
{
"hop": 1,
"source_node_id": "ERBB4",
"source_node_type": "GENE",
"source_node_label": "ERBB4",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_005235.3... | NM_005235.3(ERBB4):c.785G>A (p.Cys262Tyr) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ERBB4",
"source_db": "UniProt",
"payload": {
"accession": "Q15303",
"sequence": "MKPATGLWVWVSLLVAAGTVQPSDSQSVCAGTENKLSSLSDLEQQYRALRKYYENCEVVMGNLEITSIEHNRDLSFLRSVREVTGYVLVALNQFRYLPLENLRIIRGTKLYEDRYALAIFLNYRKDGNFGLQE... | [
{
"source_db": "ClinVar",
"source_id": "NM_005235.3(ERBB4):c.785G>A (p.Cys262Tyr)",
"text": "NM_005235.3(ERBB4):c.785G>A (p.Cys262Tyr) VARIANT_IN_GENE ERBB4",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0016996",
"text": "NM_005235.3(ERBB4):c.785G>A (p.Cys262Tyr)... | {
"gene": "ERBB4",
"disease": "NK-cell enteropathy",
"pathogenic_variants": [
"NM_005235.3(ERBB4):c.785G>A (p.Cys262Tyr)"
]
} | 0.707107 |
co_dise_00113 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in SPTLC1 are classified as Pathogenic or Likely Pathogenic for not provided? | NM_006415.4(SPTLC1):c.58G>T (p.Ala20Ser) VARIANT_IN_GENE SPTLC1 -> NM_006415.4(SPTLC1):c.58G>T (p.Ala20Ser) VARIANT_HAS_CLINICAL_SIGNIFICANCE not provided | {
"steps": [
{
"hop": 1,
"source_node_id": "SPTLC1",
"source_node_type": "GENE",
"source_node_label": "SPTLC1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_006415... | NM_006415.4(SPTLC1):c.992C>A (p.Ser331Tyr); NM_006415.4(SPTLC1):c.58G>T (p.Ala20Ser) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SPTLC1",
"source_db": "UniProt",
"payload": {
"accession": "O15269",
"sequence": "MATATEQWVLVEMVQALYEAPAYHLILEGILILWIIRLLFSKTYKLQERSDLTVKEKEELIEEWQPEPLVPPVPKDHPALNYNIVSGPPSHKTVVNGKECINFASFNFLGLLDNPRVKAAALASLKKYGVGT... | [
{
"source_db": "ClinVar",
"source_id": "NM_006415.4(SPTLC1):c.58G>T (p.Ala20Ser)",
"text": "NM_006415.4(SPTLC1):c.58G>T (p.Ala20Ser) VARIANT_IN_GENE SPTLC1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:not_provided",
"text": "NM_006415.4(SPTLC1):c.58G>T (p.Ala2... | {
"gene": "SPTLC1",
"disease": "not provided",
"pathogenic_variants": [
"NM_006415.4(SPTLC1):c.992C>A (p.Ser331Tyr)",
"NM_006415.4(SPTLC1):c.58G>T (p.Ala20Ser)"
]
} | 0.921954 |
co_dise_00114 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CHEK2 are classified as Pathogenic or Likely Pathogenic for Delayed speech and language development? | Single allele VARIANT_IN_GENE CHEK2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Delayed speech and language development | {
"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": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CHEK2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:delayed_speech_and_language_development",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Delayed speech ... | {
"gene": "CHEK2",
"disease": "Delayed speech and language development",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00115 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2C are classified as Pathogenic or Likely Pathogenic for Hypoparathyroidism, deafness, renal disease syndrome? | Single allele VARIANT_IN_GENE KMT2C -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Hypoparathyroidism, deafness, renal disease syndrome | {
"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": "Single alle... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2C",
"source_db": "UniProt",
"payload": {
"accession": "Q8NEZ4",
"sequence": "MSSEEDKSVEQPQPPPPPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGKTAVEDEDSMDGLETTETETIVETEIKEQSAEEDAEAEVDNSKQLIPTLQRSVSEESANSLVSVGVEAKISEQL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE KMT2C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:hypoparathyroidism_deafness_renal_disease_syndrome",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Hypo... | {
"gene": "KMT2C",
"disease": "Hypoparathyroidism, deafness, renal disease syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00116 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ALB are classified as Pathogenic or Likely Pathogenic for not specified? | NM_000477.7(ALB):c.1693A>G (p.Lys565Glu) VARIANT_IN_GENE ALB -> NM_000477.7(ALB):c.1693A>G (p.Lys565Glu) VARIANT_HAS_CLINICAL_SIGNIFICANCE not specified | {
"steps": [
{
"hop": 1,
"source_node_id": "ALB",
"source_node_type": "GENE",
"source_node_label": "ALB",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000477.7(ALB... | NM_000477.7(ALB):c.1693A>G (p.Lys565Glu) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ALB",
"source_db": "UniProt",
"payload": {
"accession": "P02768",
"sequence": "MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPN... | [
{
"source_db": "ClinVar",
"source_id": "NM_000477.7(ALB):c.1693A>G (p.Lys565Glu)",
"text": "NM_000477.7(ALB):c.1693A>G (p.Lys565Glu) VARIANT_IN_GENE ALB",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:not_specified",
"text": "NM_000477.7(ALB):c.1693A>G (p.Lys565G... | {
"gene": "ALB",
"disease": "not specified",
"pathogenic_variants": [
"NM_000477.7(ALB):c.1693A>G (p.Lys565Glu)"
]
} | 0.707107 |
co_dise_00117 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CREBBP are classified as Pathogenic or Likely Pathogenic for not specified? | GRCh37/hg19 16p13.3(chr16:3905233-3962938)x1 VARIANT_IN_GENE CREBBP -> GRCh37/hg19 16p13.3(chr16:3905233-3962938)x1 VARIANT_HAS_CLINICAL_SIGNIFICANCE not specified | {
"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": "GRCh37/hg... | GRCh37/hg19 16p13.3(chr16:3905233-3962938)x1; NM_004380.3(CREBBP):c.2464-2A>G | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CREBBP",
"source_db": "UniProt",
"payload": {
"accession": "Q92793",
"sequence": "MAENLLDGPPNPKRAKLSSPGFSANDSTDFGSLFDLENDLPDELIPNGGELGLLNSGNLVPDAASKHKQLSELLRGGSGSSINPGIGNVSASSPVQQGLGGQAQGQPNSANMASLSAMGKSPLSQGDSSAPS... | [
{
"source_db": "ClinVar",
"source_id": "GRCh37/hg19 16p13.3(chr16:3905233-3962938)x1",
"text": "GRCh37/hg19 16p13.3(chr16:3905233-3962938)x1 VARIANT_IN_GENE CREBBP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:not_specified",
"text": "GRCh37/hg19 16p13.3(chr16:... | {
"gene": "CREBBP",
"disease": "not specified",
"pathogenic_variants": [
"GRCh37/hg19 16p13.3(chr16:3905233-3962938)x1",
"NM_004380.3(CREBBP):c.2464-2A>G"
]
} | 0.83666 |
co_dise_00118 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in TBK1 are classified as Pathogenic or Likely Pathogenic for Primary progressive non fluent aphasia? | NM_013254.4(TBK1):c.2107G>T (p.Glu703Ter) VARIANT_IN_GENE TBK1 -> NM_013254.4(TBK1):c.2107G>T (p.Glu703Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE Primary progressive non fluent aphasia | {
"steps": [
{
"hop": 1,
"source_node_id": "TBK1",
"source_node_type": "GENE",
"source_node_label": "TBK1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_013254.4(T... | NM_013254.4(TBK1):c.2107G>T (p.Glu703Ter) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "TBK1",
"source_db": "UniProt",
"payload": {
"accession": "Q9UHD2",
"sequence": "MQSTSNHLWLLSDILGQGATANVFRGRHKKTGDLFAIKVFNNISFLRPVDVQMREFEVLKKLNHKNIVKLFAIEEETTTRHKVLIMEFCPCGSLYTVLEEPSNAYGLPESEFLIVLRDVVGGMNHLRENGIVHR... | [
{
"source_db": "ClinVar",
"source_id": "NM_013254.4(TBK1):c.2107G>T (p.Glu703Ter)",
"text": "NM_013254.4(TBK1):c.2107G>T (p.Glu703Ter) VARIANT_IN_GENE TBK1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:primary_progressive_non_fluent_aphasia",
"text": "NM_013254... | {
"gene": "TBK1",
"disease": "Primary progressive non fluent aphasia",
"pathogenic_variants": [
"NM_013254.4(TBK1):c.2107G>T (p.Glu703Ter)"
]
} | 0.707107 |
co_dise_00119 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NOTCH1 are classified as Pathogenic or Likely Pathogenic for congenital anomaly of kidney and urinary tract? | NM_017617.5(NOTCH1):c.1649dup (p.Tyr550Ter) VARIANT_IN_GENE NOTCH1 -> NM_017617.5(NOTCH1):c.1649dup (p.Tyr550Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE congenital anomaly of kidney and urinary tract | {
"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.1649dup (p.Tyr550Ter) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "ClinVar",
"source_id": "NM_017617.5(NOTCH1):c.1649dup (p.Tyr550Ter)",
"text": "NM_017617.5(NOTCH1):c.1649dup (p.Tyr550Ter) VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0019719",
"text": "NM_017617.5(NOTCH1):c.1649dup (p.Tyr... | {
"gene": "NOTCH1",
"disease": "congenital anomaly of kidney and urinary tract",
"pathogenic_variants": [
"NM_017617.5(NOTCH1):c.1649dup (p.Tyr550Ter)"
]
} | 0.921954 |
co_dise_00120 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CFAP410 are classified as Pathogenic or Likely Pathogenic for Chromosome 2q37 deletion syndrome? | Single allele VARIANT_IN_GENE CFAP410 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Chromosome 2q37 deletion syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "CFAP410",
"source_node_type": "GENE",
"source_node_label": "CFAP410",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single ... | Single allele | null | [
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CFAP410",
"source_db": "UniProt",
"payload": {
"accession": "O43822",
"sequence": "MKLTRKMVLTRAKASELHSVRKLNCWGSRLTDISICQEMPSLEVITLSVNSISTLEPVSRCQRLSELYLRRNRIPSLAELFYLKGLPRLRVLWLAENPCCGTSPHRYRMTVLRTLPRLQKLDNQAVTEEEL... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CFAP410",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:chromosome_2q37_deletion_syndrome",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Chromosome 2q37 del... | {
"gene": "CFAP410",
"disease": "Chromosome 2q37 deletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00121 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CHEK2 are classified as Pathogenic or Likely Pathogenic for pulmonary arterial hypertension? | Single allele VARIANT_IN_GENE CHEK2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE pulmonary arterial hypertension | {
"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": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CHEK2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0015924",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE pulmonary arterial hypertension",
"confidence... | {
"gene": "CHEK2",
"disease": "pulmonary arterial hypertension",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00122 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PTEN are classified as Pathogenic or Likely Pathogenic for Macrocephaly? | NM_000314.8(PTEN):c.277C>A (p.His93Asn) VARIANT_IN_GENE PTEN -> NM_000314.8(PTEN):c.277C>A (p.His93Asn) VARIANT_HAS_CLINICAL_SIGNIFICANCE Macrocephaly | {
"steps": [
{
"hop": 1,
"source_node_id": "PTEN",
"source_node_type": "GENE",
"source_node_label": "PTEN",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000314.8(P... | NM_000314.8(PTEN):c.277C>A (p.His93Asn) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PTEN",
"source_db": "UniProt",
"payload": {
"accession": "P60484",
"sequence": "MTAIIKEIVSRNKRRYQEDGFDLDLTYIYPNIIAMGFPAERLEGVYRNNIDDVVRFLDSKHKNHYKIYNLCAERHYDTAKFNCRVAQYPFEDHNPPQLELIKPFCEDLDQWLSEDDNHVAAIHCKAGKGRTGVM... | [
{
"source_db": "ClinVar",
"source_id": "NM_000314.8(PTEN):c.277C>A (p.His93Asn)",
"text": "NM_000314.8(PTEN):c.277C>A (p.His93Asn) VARIANT_IN_GENE PTEN",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:macrocephaly",
"text": "NM_000314.8(PTEN):c.277C>A (p.His93Asn)... | {
"gene": "PTEN",
"disease": "Macrocephaly",
"pathogenic_variants": [
"NM_000314.8(PTEN):c.277C>A (p.His93Asn)"
]
} | 0.921954 |
co_dise_00123 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH6 are classified as Pathogenic or Likely Pathogenic for breast-ovarian cancer, familial, susceptibility to, 1? | Single allele VARIANT_IN_GENE MSH6 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE breast-ovarian cancer, familial, susceptibility to, 1 | {
"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": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0011450",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE breast-ovarian cancer, familial, susceptibility to... | {
"gene": "MSH6",
"disease": "breast-ovarian cancer, familial, susceptibility to, 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00124 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CDH1 are classified as Pathogenic or Likely Pathogenic for colorectal cancer? | NM_004360.5(CDH1):c.1955del (p.Ile651_Leu652insTer) VARIANT_IN_GENE CDH1 -> NM_004360.5(CDH1):c.1955del (p.Ile651_Leu652insTer) VARIANT_HAS_CLINICAL_SIGNIFICANCE colorectal cancer | {
"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": "NM_004360.5(C... | NM_004360.5(CDH1):c.1955del (p.Ile651_Leu652insTer) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDH1",
"source_db": "UniProt",
"payload": {
"accession": "P12830",
"sequence": "MGPWSRSLSALLLLLQVSSWLCQEPEPCHPGFDAESYTFTVPRRHLERGRVLGRVNFEDCTGRQRTAYFSLDTRFKVGTDGVITVKRPLRFHNPQIHFLVYAWDSTYRKFSTKVTLNTVGHHHRPPPHQASVSG... | [
{
"source_db": "ClinVar",
"source_id": "NM_004360.5(CDH1):c.1955del (p.Ile651_Leu652insTer)",
"text": "NM_004360.5(CDH1):c.1955del (p.Ile651_Leu652insTer) VARIANT_IN_GENE CDH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005575",
"text": "NM_004360.5(CDH1):c.19... | {
"gene": "CDH1",
"disease": "colorectal cancer",
"pathogenic_variants": [
"NM_004360.5(CDH1):c.1955del (p.Ile651_Leu652insTer)"
]
} | 0.707107 |
co_dise_00125 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in RAD51D are classified as Pathogenic or Likely Pathogenic for RAD51D-related disorder? | NM_002878.4(RAD51D):c.340dup (p.Thr114fs) VARIANT_IN_GENE RAD51D -> NM_002878.4(RAD51D):c.340dup (p.Thr114fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE RAD51D-related disorder | {
"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.340dup (p.Thr114fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RAD51D",
"source_db": "UniProt",
"payload": {
"accession": "O75771",
"sequence": "MGVLRVGLCPGLTEEMIQLLRSHRIKTVVDLVSADLEEVAQKCGLSYKALVALRRVLLAQFSAFPVNGADLYEELKTSTAILSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCMAANVAHGLQQNV... | [
{
"source_db": "ClinVar",
"source_id": "NM_002878.4(RAD51D):c.340dup (p.Thr114fs)",
"text": "NM_002878.4(RAD51D):c.340dup (p.Thr114fs) VARIANT_IN_GENE RAD51D",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:rad51d_related_disorder",
"text": "NM_002878.4(RAD51D):c.... | {
"gene": "RAD51D",
"disease": "RAD51D-related disorder",
"pathogenic_variants": [
"NM_002878.4(RAD51D):c.340dup (p.Thr114fs)"
]
} | 0.921954 |
co_dise_00126 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ADRA2B are classified as Pathogenic or Likely Pathogenic for Marfanoid habitus and intellectual disability? | Single allele VARIANT_IN_GENE ADRA2B -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Marfanoid habitus and intellectual disability | {
"steps": [
{
"hop": 1,
"source_node_id": "ADRA2B",
"source_node_type": "GENE",
"source_node_label": "ADRA2B",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ADRA2B",
"source_db": "UniProt",
"payload": {
"accession": "P18089",
"sequence": "MDHQDPYSVQATAAIAAAITFLILFTIFGNALVILAVLTSRSLRAPQNLFLVSLAAADILVATLIIPFSLANELLGYWYFRRTWCEVYLALDVLFCTSSIVHLCAISLDRYWAVSRALEYNSKRTPRRIKCI... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ADRA2B",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:marfanoid_habitus_and_intellectual_disability",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Marfanoi... | {
"gene": "ADRA2B",
"disease": "Marfanoid habitus and intellectual disability",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00127 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2D are classified as Pathogenic or Likely Pathogenic for KBG syndrome? | Single allele VARIANT_IN_GENE KMT2D -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE KBG syndrome | {
"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": "Single alle... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2D",
"source_db": "UniProt",
"payload": {
"accession": "O14686",
"sequence": "MDSQKLAGEDKDSEPAADGPAASEDPSATESDLPNPHVGEVSVLSSGSPRLQETPQDCSGGPVRRCALCNCGEPSLHGQRELRRFELPFDWPRCPVVSPGGSPGPNEAVLPSEDLSQIGFPEGLTPAHLGEPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE KMT2D",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0007846",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE KBG syndrome",
"confidence": 0.7
}
] | {
"gene": "KMT2D",
"disease": "KBG syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00128 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ANXA11 are classified as Pathogenic or Likely Pathogenic for Kabuki syndrome 1? | Single allele VARIANT_IN_GENE ANXA11 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Kabuki syndrome 1 | {
"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": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ANXA11",
"source_db": "UniProt",
"payload": {
"accession": "P50995",
"sequence": "MSYPGYPPPPGGYPPAAPGGGPWGGAAYPPPPSMPPIGLDNVATYAGQFNQDYLSGMAANMSGTFGGANMPNLYPGAPGAGYPPVPPGGFGQPPSAQQPVPPYGMYPPPGGNPPSRMPSYPPYPGAPVPGQP... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ANXA11",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0007843",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Kabuki syndrome 1",
"confidence": 0.7
}
] | {
"gene": "ANXA11",
"disease": "Kabuki syndrome 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00129 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MYC are classified as Pathogenic or Likely Pathogenic for intellectual disability? | Single allele VARIANT_IN_GENE MYC -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE intellectual disability | {
"steps": [
{
"hop": 1,
"source_node_id": "MYC",
"source_node_type": "GENE",
"source_node_label": "MYC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MYC",
"source_db": "UniProt",
"payload": {
"accession": "P01106",
"sequence": "MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MYC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0001071",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE intellectual disability",
"confidence": 0.7
}... | {
"gene": "MYC",
"disease": "intellectual disability",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00130 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MYC are classified as Pathogenic or Likely Pathogenic for DiGeorge syndrome? | Single allele VARIANT_IN_GENE MYC -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE DiGeorge syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "MYC",
"source_node_type": "GENE",
"source_node_label": "MYC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MYC",
"source_db": "UniProt",
"payload": {
"accession": "P01106",
"sequence": "MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MYC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0008564",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE DiGeorge syndrome",
"confidence": 0.5
}
] | {
"gene": "MYC",
"disease": "DiGeorge syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00131 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NOTCH1 are classified as Pathogenic or Likely Pathogenic for Severe global developmental delay? | Single allele VARIANT_IN_GENE NOTCH1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Severe global developmental delay | {
"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": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:severe_global_developmental_delay",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Severe global develo... | {
"gene": "NOTCH1",
"disease": "Severe global developmental delay",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00132 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BARD1 are classified as Pathogenic or Likely Pathogenic for autism spectrum disorder? | Single allele VARIANT_IN_GENE BARD1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE autism spectrum disorder | {
"steps": [
{
"hop": 1,
"source_node_id": "BARD1",
"source_node_type": "GENE",
"source_node_label": "BARD1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE BARD1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005258",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE autism spectrum disorder",
"confidence": 0.7
... | {
"gene": "BARD1",
"disease": "autism spectrum disorder",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00133 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ERBB2 are classified as Pathogenic or Likely Pathogenic for colorectal cancer? | NM_004448.4(ERBB2):c.1610del (p.Gly537fs) VARIANT_IN_GENE ERBB2 -> NM_004448.4(ERBB2):c.1610del (p.Gly537fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE colorectal cancer | {
"steps": [
{
"hop": 1,
"source_node_id": "ERBB2",
"source_node_type": "GENE",
"source_node_label": "ERBB2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_004448.4... | NM_004448.4(ERBB2):c.1610del (p.Gly537fs); NM_004448.4(ERBB2):c.3484_3485insG (p.Pro1162fs) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ERBB2",
"source_db": "UniProt",
"payload": {
"accession": "P04626",
"sequence": "MELAALCRWGLLLALLPPGAASTQVCTGTDMKLRLPASPETHLDMLRHLYQGCQVVQGNLELTYLPTNASLSFLQDIQEVQGYVLIAHNQVRQVPLQRLRIVRGTQLFEDNYALAVLDNGDPLNNTTPVTGAS... | [
{
"source_db": "ClinVar",
"source_id": "NM_004448.4(ERBB2):c.1610del (p.Gly537fs)",
"text": "NM_004448.4(ERBB2):c.1610del (p.Gly537fs) VARIANT_IN_GENE ERBB2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0005575",
"text": "NM_004448.4(ERBB2):c.1610del (p.Gly537fs)... | {
"gene": "ERBB2",
"disease": "colorectal cancer",
"pathogenic_variants": [
"NM_004448.4(ERBB2):c.1610del (p.Gly537fs)",
"NM_004448.4(ERBB2):c.3484_3485insG (p.Pro1162fs)"
]
} | 0.707107 |
co_dise_00134 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in APP are classified as Pathogenic or Likely Pathogenic for Adams-Oliver syndrome 5? | Single allele VARIANT_IN_GENE APP -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Adams-Oliver syndrome 5 | {
"steps": [
{
"hop": 1,
"source_node_id": "APP",
"source_node_type": "GENE",
"source_node_label": "APP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APP",
"source_db": "UniProt",
"payload": {
"accession": "P05067",
"sequence": "MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE APP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0014459",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Adams-Oliver syndrome 5",
"confidence": 0.5
}... | {
"gene": "APP",
"disease": "Adams-Oliver syndrome 5",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00135 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACVR1 are classified as Pathogenic or Likely Pathogenic for obesity due to leptin receptor gene deficiency? | Single allele VARIANT_IN_GENE ACVR1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE obesity due to leptin receptor gene deficiency | {
"steps": [
{
"hop": 1,
"source_node_id": "ACVR1",
"source_node_type": "GENE",
"source_node_label": "ACVR1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACVR1",
"source_db": "UniProt",
"payload": {
"accession": "Q04771",
"sequence": "MVDGVMILPVLIMIALPSPSMEDEKPKVNPKLYMCVCEGLSCGNEDHCEGQQCFSSLSINDGFHVYQKGCFQVYEQGKMTCKTPPSPGQAVECCQGDWCNRNITAQLPTKGKSFPGTQNFHLEVGLIILSVVF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ACVR1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013992",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE obesity due to leptin receptor gene deficiency",
... | {
"gene": "ACVR1",
"disease": "obesity due to leptin receptor gene deficiency",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00136 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ATM are classified as Pathogenic or Likely Pathogenic for chromosome 16q22 deletion syndrome? | Single allele VARIANT_IN_GENE ATM -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE chromosome 16q22 deletion syndrome | {
"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": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATM",
"source_db": "UniProt",
"payload": {
"accession": "Q13315",
"sequence": "MSLVLNDLLICCRQLEHDRATERKKEVEKFKRLIRDPETIKHLDRHSDSKQGKYLNWDAVFRFLQKYIQKETECLRIAKPNVSASTQASRQKKMQEISSLVKYFIKCANRRAPRLKCQELLNYIMDTVKDSSNGA... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ATM",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013798",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE chromosome 16q22 deletion syndrome",
"confidenc... | {
"gene": "ATM",
"disease": "chromosome 16q22 deletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00137 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BRCA2 are classified as Pathogenic or Likely Pathogenic for not specified? | NM_000059.4(BRCA2):c.5511dup (p.Glu1838Ter) VARIANT_IN_GENE BRCA2 -> NM_000059.4(BRCA2):c.5511dup (p.Glu1838Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE not specified | {
"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.5511dup (p.Glu1838Ter); NM_000059.4(BRCA2):c.7292dup (p.Asn2431fs) | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA2",
"source_db": "UniProt",
"payload": {
"accession": "P51587",
"sequence": "MPIGSKERPTFFEIFKTRCNKADLGPISLNWFEELSSEAPPYNSEPAEESEHKNNNYEPNLFKTPQRKPSYNQLASTPIIFKEQGLTLPLYQSPVKELDKFKLDLGRNVPNSRHKSLRTVKTKMDQADDVSCP... | [
{
"source_db": "ClinVar",
"source_id": "NM_000059.4(BRCA2):c.5511dup (p.Glu1838Ter)",
"text": "NM_000059.4(BRCA2):c.5511dup (p.Glu1838Ter) VARIANT_IN_GENE BRCA2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:not_specified",
"text": "NM_000059.4(BRCA2):c.5511dup ... | {
"gene": "BRCA2",
"disease": "not specified",
"pathogenic_variants": [
"NM_000059.4(BRCA2):c.5511dup (p.Glu1838Ter)",
"NM_000059.4(BRCA2):c.7292dup (p.Asn2431fs)"
]
} | 0.921954 |
co_dise_00138 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in SYNJ1 are classified as Pathogenic or Likely Pathogenic for early-onset Parkinson disease 20? | NC_000021.9:g.(?_32727926)_(32728060_?)del VARIANT_IN_GENE SYNJ1 -> NC_000021.9:g.(?_32727926)_(32728060_?)del VARIANT_HAS_CLINICAL_SIGNIFICANCE early-onset Parkinson disease 20 | {
"steps": [
{
"hop": 1,
"source_node_id": "SYNJ1",
"source_node_type": "GENE",
"source_node_label": "SYNJ1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NC_000021.9... | NM_203446.3(SYNJ1):c.3526C>T (p.Gln1176Ter); NM_203446.3(SYNJ1):c.2242_2243del (p.Gln748fs); NC_000021.9:g.(?_32727926)_(32728060_?)del; NM_203446.3(SYNJ1):c.1213C>T (p.Gln405Ter); NM_003895.4(SYNJ1):c.8del (p.Lys3fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SYNJ1",
"source_db": "UniProt",
"payload": {
"accession": "O43426",
"sequence": "MAFSKGFRIYHKLDPPPFSLIVETRHKEECLMFESGAVAVLSSAEKEAIKGTYSKVLDAYGLLGVLRLNLGDTMLHYLVLVTGCMSVGKIQESEVFRVTSTEFISLRIDSSDEDRISEVRKVLNSGNFYFAWS... | [
{
"source_db": "ClinVar",
"source_id": "NC_000021.9:g.(?_32727926)_(32728060_?)del",
"text": "NC_000021.9:g.(?_32727926)_(32728060_?)del VARIANT_IN_GENE SYNJ1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0014233",
"text": "NC_000021.9:g.(?_32727926)_(32728060_?)... | {
"gene": "SYNJ1",
"disease": "early-onset Parkinson disease 20",
"pathogenic_variants": [
"NM_203446.3(SYNJ1):c.3526C>T (p.Gln1176Ter)",
"NM_203446.3(SYNJ1):c.2242_2243del (p.Gln748fs)",
"NC_000021.9:g.(?_32727926)_(32728060_?)del",
"NM_203446.3(SYNJ1):c.1213C>T (p.Gln405Ter)",
"NM_003895.4(S... | 0.83666 |
co_dise_00139 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH6 are classified as Pathogenic or Likely Pathogenic for obesity due to leptin receptor gene deficiency? | Single allele VARIANT_IN_GENE MSH6 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE obesity due to leptin receptor gene deficiency | {
"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": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013992",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE obesity due to leptin receptor gene deficiency",
... | {
"gene": "MSH6",
"disease": "obesity due to leptin receptor gene deficiency",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00140 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH6 are classified as Pathogenic or Likely Pathogenic for Li-Fraumeni syndrome? | Single allele VARIANT_IN_GENE MSH6 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Li-Fraumeni 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": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0018875",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Li-Fraumeni syndrome",
"confidence": 0.7
}
] | {
"gene": "MSH6",
"disease": "Li-Fraumeni syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00141 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACKR3 are classified as Pathogenic or Likely Pathogenic for 9p partial trisomy syndrome? | Single allele VARIANT_IN_GENE ACKR3 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 9p partial trisomy syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "ACKR3",
"source_node_type": "GENE",
"source_node_label": "ACKR3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACKR3",
"source_db": "UniProt",
"payload": {
"accession": "P25106",
"sequence": "MDLHLFDYSEPGNFSDISWPCNSSDCIVVDTVMCPNMPNKSVLLYTLSFIYIFIFVIGMIANSVVVWVNIQAKTTGYDTHCYILNLAIADLWVVLTIPVWVVSLVQHNQWPMGELTCKVTHLIFSINLFGSIF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE ACKR3",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:9p_partial_trisomy_syndrome",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE 9p partial trisomy syndrome... | {
"gene": "ACKR3",
"disease": "9p partial trisomy syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00142 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BRCA1 are classified as Pathogenic or Likely Pathogenic for Deletion of long arm of chromosome 18? | Single allele VARIANT_IN_GENE BRCA1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Deletion of long arm of chromosome 18 | {
"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": "Single alle... | Single allele | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE BRCA1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:deletion_of_long_arm_of_chromosome_18",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Deletion of long ... | {
"gene": "BRCA1",
"disease": "Deletion of long arm of chromosome 18",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00143 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NOTCH1 are classified as Pathogenic or Likely Pathogenic for neurodevelopmental disorder? | Single allele VARIANT_IN_GENE NOTCH1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE neurodevelopmental 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": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NOTCH1",
"source_db": "UniProt",
"payload": {
"accession": "P46531",
"sequence": "MPPLLAPLLCLALLPALAARGPRCSQPGETCLNGGKCEAANGTEACVCGGAFVGPRCQDPNPCLSTPCKNAGTCHVVDRRGVADYACSCALGFSGPLCLTPLDNACLTNPCRNGGTCDLLTLTEYKCRCPPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE NOTCH1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0700092",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE neurodevelopmental disorder",
"confidence": ... | {
"gene": "NOTCH1",
"disease": "neurodevelopmental disorder",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00144 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PSEN1 are 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 | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PSEN1",
"source_db": "UniProt",
"payload": {
"accession": "P49768",
"sequence": "MTELPAPLSYFQNAQMSEDNHLSNTVRSQNDNRERQEHNDRRSLGHPEPLSNGRPQGNSRQVVEQDEEEDEELTLKYGAKHVIMLFVPVTLCMVVVVATIKSVSFYTRKDGQLIYTPFTEDTETVGQRALHSI... | [
{
"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": "MONDO:0011743",
"text": "NM_000021.4(PSEN1):c.869-1624_956-2452del... | {
"gene": "PSEN1",
"disease": "Alzheimer disease 4",
"pathogenic_variants": [
"NM_000021.4(PSEN1):c.869-1624_956-2452del"
]
} | 0.707107 |
co_dise_00145 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH2 are classified as Pathogenic or Likely Pathogenic for neurofibromatosis type 1? | Single allele VARIANT_IN_GENE MSH2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE neurofibromatosis type 1 | {
"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": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH2",
"source_db": "UniProt",
"payload": {
"accession": "P43246",
"sequence": "MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDI... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0018975",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE neurofibromatosis type 1",
"confidence": 0.7
... | {
"gene": "MSH2",
"disease": "neurofibromatosis type 1",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00146 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BAX are classified as Pathogenic or Likely Pathogenic for T-cell acute lymphoblastic leukemia? | NM_138761.4(BAX):c.115_121del (p.Gly39fs) VARIANT_IN_GENE BAX -> NM_138761.4(BAX):c.115_121del (p.Gly39fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE T-cell acute lymphoblastic leukemia | {
"steps": [
{
"hop": 1,
"source_node_id": "BAX",
"source_node_type": "GENE",
"source_node_label": "BAX",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_138761.4(BAX... | NM_138761.4(BAX):c.115_121del (p.Gly39fs); NM_138761.4(BAX):c.199G>A (p.Gly67Arg) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BAX",
"source_db": "UniProt",
"payload": {
"accession": "Q07812",
"sequence": "MDGSGEQPRGGGPTSSEQIMKTGALLLQGFIQDRAGRMGGEAPELALDPVPQDASTKKLSECLKRIGDELDSNMELQRMIAAVDTDSPREVFFRVAADMFSDGNFNWGRVVALFYFASKLVLKALCTKVPELIRT... | [
{
"source_db": "ClinVar",
"source_id": "NM_138761.4(BAX):c.115_121del (p.Gly39fs)",
"text": "NM_138761.4(BAX):c.115_121del (p.Gly39fs) VARIANT_IN_GENE BAX",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0004963",
"text": "NM_138761.4(BAX):c.115_121del (p.Gly39fs) V... | {
"gene": "BAX",
"disease": "T-cell acute lymphoblastic leukemia",
"pathogenic_variants": [
"NM_138761.4(BAX):c.115_121del (p.Gly39fs)",
"NM_138761.4(BAX):c.199G>A (p.Gly67Arg)"
]
} | 0.707107 |
co_dise_00147 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BRAF are classified as Pathogenic or Likely Pathogenic for RASopathy? | NM_004333.6(BRAF):c.1781A>T (p.Asp594Val) VARIANT_IN_GENE BRAF -> NM_004333.6(BRAF):c.1781A>T (p.Asp594Val) VARIANT_HAS_CLINICAL_SIGNIFICANCE RASopathy | {
"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.1591T>C (p.Trp531Arg); NM_004333.6(BRAF):c.823G>A (p.Glu275Lys); NM_004333.6(BRAF):c.1448A>C (p.Lys483Thr); NM_004333.6(BRAF):c.1781A>T (p.Asp594Val); NM_004333.6(BRAF):c.1796C>G (p.Thr599Arg) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRAF",
"source_db": "UniProt",
"payload": {
"accession": "P15056",
"sequence": "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEHIEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTVTSSSSSSLSVLPSS... | [
{
"source_db": "ClinVar",
"source_id": "NM_004333.6(BRAF):c.1781A>T (p.Asp594Val)",
"text": "NM_004333.6(BRAF):c.1781A>T (p.Asp594Val) VARIANT_IN_GENE BRAF",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0021060",
"text": "NM_004333.6(BRAF):c.1781A>T (p.Asp594Val) ... | {
"gene": "BRAF",
"disease": "RASopathy",
"pathogenic_variants": [
"NM_004333.6(BRAF):c.1591T>C (p.Trp531Arg)",
"NM_004333.6(BRAF):c.823G>A (p.Glu275Lys)",
"NM_004333.6(BRAF):c.1448A>C (p.Lys483Thr)",
"NM_004333.6(BRAF):c.1781A>T (p.Asp594Val)",
"NM_004333.6(BRAF):c.1796C>G (p.Thr599Arg)",
... | 0.974679 |
co_dise_00148 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in PALB2 are classified as Pathogenic or Likely Pathogenic for gastric cancer? | NM_024675.4(PALB2):c.2T>A (p.Met1Lys) VARIANT_IN_GENE PALB2 -> NM_024675.4(PALB2):c.2T>A (p.Met1Lys) VARIANT_HAS_CLINICAL_SIGNIFICANCE gastric 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.659del (p.Ser220fs); NM_024675.4(PALB2):c.2T>A (p.Met1Lys) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PALB2",
"source_db": "UniProt",
"payload": {
"accession": "Q86YC2",
"sequence": "MDEPPGKPLSCEEKEKLKEKLAFLKREYSKTLARLQRAQRAEKIKHSIKKTVEEQDCLSQQDLSPQLKHSEPKNKICVYDKLHIKTHLDEETGEKTSITLDVGPESFNPGDGPGGLPIQRTDDTQEHFPHRVS... | [
{
"source_db": "ClinVar",
"source_id": "NM_024675.4(PALB2):c.2T>A (p.Met1Lys)",
"text": "NM_024675.4(PALB2):c.2T>A (p.Met1Lys) VARIANT_IN_GENE PALB2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0001056",
"text": "NM_024675.4(PALB2):c.2T>A (p.Met1Lys) VARIANT_HAS... | {
"gene": "PALB2",
"disease": "gastric cancer",
"pathogenic_variants": [
"NM_024675.4(PALB2):c.659del (p.Ser220fs)",
"NM_024675.4(PALB2):c.2T>A (p.Met1Lys)"
]
} | 0.707107 |
co_dise_00149 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in LEPR are classified as Pathogenic or Likely Pathogenic for glioma? | Single allele VARIANT_IN_GENE LEPR -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE glioma | {
"steps": [
{
"hop": 1,
"source_node_id": "LEPR",
"source_node_type": "GENE",
"source_node_label": "LEPR",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "LEPR",
"source_db": "UniProt",
"payload": {
"accession": "P48357",
"sequence": "MICQKFCVVLLHWEFIYVITAFNLSYPITPWRFKLSCMPPNSTYDYFLLPAGLSKNTSNSNGHYETAVEPKFNSSGTHFSNLSKTTFHCCFRSEQDRNCSLCADNIEGKTFVSTVNSLVFQQIDANWNIQCWLK... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE LEPR",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0021042",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE glioma",
"confidence": 0.5
}
] | {
"gene": "LEPR",
"disease": "glioma",
"pathogenic_variants": [
"Single allele"
]
} | 0.707107 |
co_dise_00150 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ATP6V1A are classified as Pathogenic or Likely Pathogenic for Cerebral visual impairment and intellectual disability? | NM_001690.4(ATP6V1A):c.940A>G (p.Asn314Asp) VARIANT_IN_GENE ATP6V1A -> NM_001690.4(ATP6V1A):c.940A>G (p.Asn314Asp) VARIANT_HAS_CLINICAL_SIGNIFICANCE Cerebral visual impairment and intellectual disability | {
"steps": [
{
"hop": 1,
"source_node_id": "ATP6V1A",
"source_node_type": "GENE",
"source_node_label": "ATP6V1A",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_0016... | NM_001690.4(ATP6V1A):c.940A>G (p.Asn314Asp) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATP6V1A",
"source_db": "UniProt",
"payload": {
"accession": "P38606",
"sequence": "MDFSKLPKILDEDKESTFGYVHGVSGPVVTACDMAGAAMYELVRVGHSELVGEIIRLEGDMATIQVYEETSGVSVGDPVLRTGKPLSVELGPGIMGAIFDGIQRPLSDISSQTQSIYIPRGVNVSALSRDI... | [
{
"source_db": "ClinVar",
"source_id": "NM_001690.4(ATP6V1A):c.940A>G (p.Asn314Asp)",
"text": "NM_001690.4(ATP6V1A):c.940A>G (p.Asn314Asp) VARIANT_IN_GENE ATP6V1A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:cerebral_visual_impairment_and_intellectual_disability",... | {
"gene": "ATP6V1A",
"disease": "Cerebral visual impairment and intellectual disability",
"pathogenic_variants": [
"NM_001690.4(ATP6V1A):c.940A>G (p.Asn314Asp)"
]
} | 0.921954 |
co_dise_00151 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CHEK2 are classified as Pathogenic or Likely Pathogenic for tricho-dento-osseous syndrome? | Single allele VARIANT_IN_GENE CHEK2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE tricho-dento-osseous syndrome | {
"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": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CHEK2",
"source_db": "UniProt",
"payload": {
"accession": "O96017",
"sequence": "MSRESDVEAQQSHGSSACSQPHGSVTQSQGSSSQSQGISSSSTSTMPNSSQSSHSSSGTLSSLETVSTQELYSIPEDQEPEDQEPEEPTPAPWARLWALQDGFANLECVNDNYWFGRDKSCEYCFDEPLLKRT... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CHEK2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0008592",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE tricho-dento-osseous syndrome",
"confidence":... | {
"gene": "CHEK2",
"disease": "tricho-dento-osseous syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00152 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in SLC18A2 are classified as Pathogenic or Likely Pathogenic for Abnormal dense granules? | NM_003054.6(SLC18A2):c.946C>G (p.Pro316Ala) VARIANT_IN_GENE SLC18A2 -> NM_003054.6(SLC18A2):c.946C>G (p.Pro316Ala) VARIANT_HAS_CLINICAL_SIGNIFICANCE Abnormal dense granules | {
"steps": [
{
"hop": 1,
"source_node_id": "SLC18A2",
"source_node_type": "GENE",
"source_node_label": "SLC18A2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_0030... | NM_003054.6(SLC18A2):c.946C>G (p.Pro316Ala) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "SLC18A2",
"source_db": "UniProt",
"payload": {
"accession": "Q05940",
"sequence": "MALSELALVRWLQESRRSRKLILFIVFLALLLDNMLLTVVVPIIPSYLYSIKHEKNATEIQTARPVHTASISDSFQSIFSYYDNSTMVTGNATRDLTLHQTATQHMVTNASAVPSDCPSEDKDLLNENVQV... | [
{
"source_db": "ClinVar",
"source_id": "NM_003054.6(SLC18A2):c.946C>G (p.Pro316Ala)",
"text": "NM_003054.6(SLC18A2):c.946C>G (p.Pro316Ala) VARIANT_IN_GENE SLC18A2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:abnormal_dense_granules",
"text": "NM_003054.6(SLC18... | {
"gene": "SLC18A2",
"disease": "Abnormal dense granules",
"pathogenic_variants": [
"NM_003054.6(SLC18A2):c.946C>G (p.Pro316Ala)"
]
} | 0.707107 |
co_dise_00153 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BRCA1 are 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.2850_2851del (p.Arg951fs); NM_007294.4(BRCA1):c.135-1G>A; NM_007294.4(BRCA1):c.5057A>G (p.His1686Arg) | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"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 |
co_dise_00154 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in KMT2C are classified as Pathogenic or Likely Pathogenic for plasma cell myeloma? | NM_170606.3(KMT2C):c.9181C>G (p.Gln3061Glu) VARIANT_IN_GENE KMT2C -> NM_170606.3(KMT2C):c.9181C>G (p.Gln3061Glu) VARIANT_HAS_CLINICAL_SIGNIFICANCE plasma cell myeloma | {
"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.9137T>C (p.Leu3046Pro); NM_170606.3(KMT2C):c.9181C>G (p.Gln3061Glu) | null | [
"expression",
"protein_sequence"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "KMT2C",
"source_db": "UniProt",
"payload": {
"accession": "Q8NEZ4",
"sequence": "MSSEEDKSVEQPQPPPPPPEEPGAPAPSPAAADKRPRGRPRKDGASPFQRARKKPRSRGKTAVEDEDSMDGLETTETETIVETEIKEQSAEEDAEAEVDNSKQLIPTLQRSVSEESANSLVSVGVEAKISEQL... | [
{
"source_db": "ClinVar",
"source_id": "NM_170606.3(KMT2C):c.9181C>G (p.Gln3061Glu)",
"text": "NM_170606.3(KMT2C):c.9181C>G (p.Gln3061Glu) VARIANT_IN_GENE KMT2C",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0009693",
"text": "NM_170606.3(KMT2C):c.9181C>G (p.Gln30... | {
"gene": "KMT2C",
"disease": "plasma cell myeloma",
"pathogenic_variants": [
"NM_170606.3(KMT2C):c.9137T>C (p.Leu3046Pro)",
"NM_170606.3(KMT2C):c.9181C>G (p.Gln3061Glu)"
]
} | 0.707107 |
co_dise_00155 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CD274 are classified as Pathogenic or Likely Pathogenic for partial duplication of the short arm of chromosome 3? | Single allele VARIANT_IN_GENE CD274 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE partial duplication of the short arm of chromosome 3 | {
"steps": [
{
"hop": 1,
"source_node_id": "CD274",
"source_node_type": "GENE",
"source_node_label": "CD274",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single alle... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CD274",
"source_db": "UniProt",
"payload": {
"accession": "Q9NZQ7",
"sequence": "MRIFAVFIFMTYWHLLNAFTVTVPKDLYVVEYGSNMTIECKFPVEKQLDLAALIVYWEMEDKNIIQFVHGEEDLKVQHSSYRQRARLLKDQLSLGNAALQITDVKLQDAGVYRCMISYGGADYKRITVKVNAP... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CD274",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0016940",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE partial duplication of the short arm of chromosom... | {
"gene": "CD274",
"disease": "partial duplication of the short arm of chromosome 3",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00156 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CDKN2A are classified as Pathogenic or Likely Pathogenic for Rubinstein-Taybi syndrome due to CREBBP mutations? | Single allele VARIANT_IN_GENE CDKN2A -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Rubinstein-Taybi syndrome due to CREBBP mutations | {
"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": "Single al... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDKN2A",
"source_db": "UniProt",
"payload": {
"accession": "Q8N726",
"sequence": "MVRRFLVTLRIRRACGPPRVRVFVVHIPRLTGEWAAPGAPAAVALVLMLLRSQRLGQQPLPRRPGHDDGQRPSGGAAAAPRRGAQLRRPRHSHPTRARRCPGGLPGHAGGAAPGRGAAGRARCLGPSARGPG... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE CDKN2A",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0008393",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Rubinstein-Taybi syndrome due to CREBBP mutation... | {
"gene": "CDKN2A",
"disease": "Rubinstein-Taybi syndrome due to CREBBP mutations",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00157 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ALS2 are classified as Pathogenic or Likely Pathogenic for Limb dystonia? | NC_000002.12:g.201705201del VARIANT_IN_GENE ALS2 -> NC_000002.12:g.201705201del VARIANT_HAS_CLINICAL_SIGNIFICANCE Limb dystonia | {
"steps": [
{
"hop": 1,
"source_node_id": "ALS2",
"source_node_type": "GENE",
"source_node_label": "ALS2",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NC_000002.12:... | NC_000002.12:g.201705201del | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ALS2",
"source_db": "UniProt",
"payload": {
"accession": "Q96Q42",
"sequence": "MDSKKRSSTEAEGSKERGLVHIWQAGSFPITPERLPGWGGKTVLQAALGVKHGVLLTEDGEVYSFGTLPWRSGPVEICPSSPILENALVGQYVITVATGSFHSGAVTDNGVAYMWGENSAGQCAVANQQYVPEP... | [
{
"source_db": "ClinVar",
"source_id": "NC_000002.12:g.201705201del",
"text": "NC_000002.12:g.201705201del VARIANT_IN_GENE ALS2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:limb_dystonia",
"text": "NC_000002.12:g.201705201del VARIANT_HAS_CLINICAL_SIGNIFICANCE ... | {
"gene": "ALS2",
"disease": "Limb dystonia",
"pathogenic_variants": [
"NC_000002.12:g.201705201del"
]
} | 0.707107 |
co_dise_00158 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in APP are classified as Pathogenic or Likely Pathogenic for nemaline myopathy 6? | Single allele VARIANT_IN_GENE APP -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE nemaline myopathy 6 | {
"steps": [
{
"hop": 1,
"source_node_id": "APP",
"source_node_type": "GENE",
"source_node_label": "APP",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "APP",
"source_db": "UniProt",
"payload": {
"accession": "P05067",
"sequence": "MLPGLALLLLAAWTARALEVPTDGNAGLLAEPQIAMFCGRLNMHMNVQNGKWDSDPSGTKTCIDTKEGILQYCQEVYPELQITNVVEANQPVTIQNWCKRGRKQCKTHPHFVIPYRCLVGEFVSDALLVPDKCKF... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE APP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0012237",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE nemaline myopathy 6",
"confidence": 0.7
}
] | {
"gene": "APP",
"disease": "nemaline myopathy 6",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00159 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in AFP are classified as Pathogenic or Likely Pathogenic for Alpha-fetoprotein deficiency? | NM_001134.3(AFP):c.543G>A (p.Trp181Ter) VARIANT_IN_GENE AFP -> NM_001134.3(AFP):c.543G>A (p.Trp181Ter) 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.543G>A (p.Trp181Ter); NM_001134.3(AFP):c.883_884del (p.Leu295fs) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AFP",
"source_db": "UniProt",
"payload": {
"accession": "P02771",
"sequence": "MKWVESIFLIFLLNFTESRTLHRNEYGIASILDSYQCTAEISLADLATIFFAQFVQEATYKEVSKMVKDALTAIEKPTGDEQSSGCLENQLPAFLEELCHEKEILEKYGHSDCCSQSEEGRHNCFLAHKKPTPAS... | [
{
"source_db": "ClinVar",
"source_id": "NM_001134.3(AFP):c.543G>A (p.Trp181Ter)",
"text": "NM_001134.3(AFP):c.543G>A (p.Trp181Ter) VARIANT_IN_GENE AFP",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:alpha_fetoprotein_deficiency",
"text": "NM_001134.3(AFP):c.543G>... | {
"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 |
co_dise_00160 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BRCA1 are classified as Pathogenic or Likely Pathogenic for ZTTK syndrome? | Single allele VARIANT_IN_GENE BRCA1 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE ZTTK syndrome | {
"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": "Single alle... | Single allele | null | [
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BRCA1",
"source_db": "UniProt",
"payload": {
"accession": "P38398",
"sequence": "MDLSALRVEEVQNVINAMQKILECPICLELIKEPVSTKCDHIFCKFCMLKLLNQKKGPSQCPLCKNDITKRSLQESTRFSQLVEELLKIICAFQLDTGLEYANSYNFAKKENNSPEHLKDEVSIIQSMGYRNR... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE BRCA1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0014936",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE ZTTK syndrome",
"confidence": 0.7
}
] | {
"gene": "BRCA1",
"disease": "ZTTK syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00161 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in RAD51D are classified as Pathogenic or Likely Pathogenic for ovarian neoplasm? | NM_002878.4(RAD51D):c.345+1G>A VARIANT_IN_GENE RAD51D -> NM_002878.4(RAD51D):c.345+1G>A VARIANT_HAS_CLINICAL_SIGNIFICANCE ovarian neoplasm | {
"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.345+1G>A | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "RAD51D",
"source_db": "UniProt",
"payload": {
"accession": "O75771",
"sequence": "MGVLRVGLCPGLTEEMIQLLRSHRIKTVVDLVSADLEEVAQKCGLSYKALVALRRVLLAQFSAFPVNGADLYEELKTSTAILSTGIGSLDKLLDAGLYTGEVTEIVGGPGSGKTQVCLCMAANVAHGLQQNV... | [
{
"source_db": "ClinVar",
"source_id": "NM_002878.4(RAD51D):c.345+1G>A",
"text": "NM_002878.4(RAD51D):c.345+1G>A VARIANT_IN_GENE RAD51D",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0021068",
"text": "NM_002878.4(RAD51D):c.345+1G>A VARIANT_HAS_CLINICAL_SIGNIFICAN... | {
"gene": "RAD51D",
"disease": "ovarian neoplasm",
"pathogenic_variants": [
"NM_002878.4(RAD51D):c.345+1G>A"
]
} | 0.707107 |
co_dise_00162 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in NEFL are classified as Pathogenic or Likely Pathogenic for Charcot-Marie-Tooth disease, dominant intermediate G? | NM_006158.5(NEFL):c.292A>C (p.Asn98His) VARIANT_IN_GENE NEFL -> NM_006158.5(NEFL):c.292A>C (p.Asn98His) VARIANT_HAS_CLINICAL_SIGNIFICANCE Charcot-Marie-Tooth disease, dominant intermediate G | {
"steps": [
{
"hop": 1,
"source_node_id": "NEFL",
"source_node_type": "GENE",
"source_node_label": "NEFL",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_006158.5(N... | NM_006158.5(NEFL):c.292A>C (p.Asn98His) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "NEFL",
"source_db": "UniProt",
"payload": {
"accession": "P07196",
"sequence": "MSSFSYEPYYSTSYKRRYVETPRVHISSVRSGYSTARSAYSSYSAPVSSSLSVRRSYSSSSGSLMPSLENLDLSQVAAISNDLKSIRTQEKAQLQDLNDRFASFIERVHELEQQNKVLEAELLVLRQKHSEPSR... | [
{
"source_db": "ClinVar",
"source_id": "NM_006158.5(NEFL):c.292A>C (p.Asn98His)",
"text": "NM_006158.5(NEFL):c.292A>C (p.Asn98His) VARIANT_IN_GENE NEFL",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0036484",
"text": "NM_006158.5(NEFL):c.292A>C (p.Asn98His) VARIAN... | {
"gene": "NEFL",
"disease": "Charcot-Marie-Tooth disease, dominant intermediate G",
"pathogenic_variants": [
"NM_006158.5(NEFL):c.292A>C (p.Asn98His)"
]
} | 0.921954 |
co_dise_00163 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH6 are classified as Pathogenic or Likely Pathogenic for hereditary nonpolyposis colon cancer? | NM_000179.3(MSH6):c.1805C>A (p.Ser602Ter) VARIANT_IN_GENE MSH6 -> NM_000179.3(MSH6):c.1805C>A (p.Ser602Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE hereditary nonpolyposis colon 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.2276_2277del (p.Leu759fs); NM_000179.3(MSH6):c.3705_3708del (p.Ala1236fs); NM_000179.3(MSH6):c.3700del (p.Glu1234fs); NM_000179.3(MSH6):c.3605_3614del (p.Met1202fs); NM_000179.3(MSH6):c.3252_3253insC (p.Thr1085fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH6",
"source_db": "UniProt",
"payload": {
"accession": "P52701",
"sequence": "MSRQSTLYSFFPKSPALSDANKASARASREGGRAAAAPGASPSPGGDAAWSEAGPGPRPLARSASPPKAKNLNGGLRRSVAPAAPTSCDFSPGDLVWAKMEGYPWWPCLVYNHPFDGTFIREKGKSVRVHVQFF... | [
{
"source_db": "ClinVar",
"source_id": "NM_000179.3(MSH6):c.1805C>A (p.Ser602Ter)",
"text": "NM_000179.3(MSH6):c.1805C>A (p.Ser602Ter) VARIANT_IN_GENE MSH6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0018630",
"text": "NM_000179.3(MSH6):c.1805C>A (p.Ser602Ter) ... | {
"gene": "MSH6",
"disease": "hereditary nonpolyposis colon cancer",
"pathogenic_variants": [
"NM_000179.3(MSH6):c.2276_2277del (p.Leu759fs)",
"NM_000179.3(MSH6):c.3705_3708del (p.Ala1236fs)",
"NM_000179.3(MSH6):c.3700del (p.Glu1234fs)",
"NM_000179.3(MSH6):c.3605_3614del (p.Met1202fs)",
"NM_00... | 0.921954 |
co_dise_00164 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MSH2 are classified as Pathogenic or Likely Pathogenic for obesity due to leptin receptor gene deficiency? | Single allele VARIANT_IN_GENE MSH2 -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE obesity due to leptin receptor gene deficiency | {
"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": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MSH2",
"source_db": "UniProt",
"payload": {
"accession": "P43246",
"sequence": "MAVQPKETLQLESAAEVGFVRFFQGMPEKPTTTVRLFDRGDFYTAHGEDALLAAREVFKTQGVIKYMGPAGAKNLQSVVLSKMNFESFVKDLLLVRQYRVEVYKNRAGNKASKENDWYLAYKASPGNLSQFEDI... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MSH2",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0013992",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE obesity due to leptin receptor gene deficiency",
... | {
"gene": "MSH2",
"disease": "obesity due to leptin receptor gene deficiency",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00165 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ACE are classified as Pathogenic or Likely Pathogenic for renal tubular dysgenesis of genetic origin? | NM_000789.4(ACE):c.207G>A (p.Trp69Ter) VARIANT_IN_GENE ACE -> NM_000789.4(ACE):c.207G>A (p.Trp69Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE renal tubular dysgenesis of genetic origin | {
"steps": [
{
"hop": 1,
"source_node_id": "ACE",
"source_node_type": "GENE",
"source_node_label": "ACE",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000789.4(ACE... | NM_000789.4(ACE):c.207G>A (p.Trp69Ter); NM_000789.4(ACE):c.3409C>T (p.Gln1137Ter); NM_000789.4(ACE):c.2T>C (p.Met1Thr); NM_000789.4(ACE):c.1473_1475delinsA (p.Asp491fs); NM_000789.4(ACE):c.1522C>T (p.Arg508Ter) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACE",
"source_db": "UniProt",
"payload": {
"accession": "P12821",
"sequence": "MGAASGRRGPGLLLPLPLLLLLPPQPALALDPGLQPGNFSADEAGAQLFAQSYNSSAEQVLFQSVAASWAHDTNITAENARRQEEAALLSQEFAEAWGQKAKELYEPIWQNFTDPQLRRIIGAVRTLGSANLPLA... | [
{
"source_db": "ClinVar",
"source_id": "NM_000789.4(ACE):c.207G>A (p.Trp69Ter)",
"text": "NM_000789.4(ACE):c.207G>A (p.Trp69Ter) VARIANT_IN_GENE ACE",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0009970",
"text": "NM_000789.4(ACE):c.207G>A (p.Trp69Ter) VARIANT_HA... | {
"gene": "ACE",
"disease": "renal tubular dysgenesis of genetic origin",
"pathogenic_variants": [
"NM_000789.4(ACE):c.207G>A (p.Trp69Ter)",
"NM_000789.4(ACE):c.3409C>T (p.Gln1137Ter)",
"NM_000789.4(ACE):c.2T>C (p.Met1Thr)",
"NM_000789.4(ACE):c.1473_1475delinsA (p.Asp491fs)",
"NM_000789.4(ACE)... | 0.83666 |
co_dise_00166 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in MYC are classified as Pathogenic or Likely Pathogenic for distal 10q deletion syndrome? | Single allele VARIANT_IN_GENE MYC -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE distal 10q deletion syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "MYC",
"source_node_type": "GENE",
"source_node_label": "MYC",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele",... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MYC",
"source_db": "UniProt",
"payload": {
"accession": "P01106",
"sequence": "MDFFRVVENQQPPATMPLNVSFTNRNYDLDYDSVQPYFYCDEEENFYQQQQQSELQPPAPSEDIWKKFELLPTPPLSPSRRSGLCSPSYVAVTPFSLRGDNDGGGGSFSTADQLEMVTELLGGDMVNQSFICDPD... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE MYC",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0012315",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE distal 10q deletion syndrome",
"confidence": 0.... | {
"gene": "MYC",
"disease": "distal 10q deletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00167 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in LEPR are classified as Pathogenic or Likely Pathogenic for Chromosome 2q37 deletion syndrome? | Single allele VARIANT_IN_GENE LEPR -> Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Chromosome 2q37 deletion syndrome | {
"steps": [
{
"hop": 1,
"source_node_id": "LEPR",
"source_node_type": "GENE",
"source_node_label": "LEPR",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "Single allele... | Single allele | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "LEPR",
"source_db": "UniProt",
"payload": {
"accession": "P48357",
"sequence": "MICQKFCVVLLHWEFIYVITAFNLSYPITPWRFKLSCMPPNSTYDYFLLPAGLSKNTSNSNGHYETAVEPKFNSSGTHFSNLSKTTFHCCFRSEQDRNCSLCADNIEGKTFVSTVNSLVFQQIDANWNIQCWLK... | [
{
"source_db": "ClinVar",
"source_id": "Single allele",
"text": "Single allele VARIANT_IN_GENE LEPR",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:chromosome_2q37_deletion_syndrome",
"text": "Single allele VARIANT_HAS_CLINICAL_SIGNIFICANCE Chromosome 2q37 deleti... | {
"gene": "LEPR",
"disease": "Chromosome 2q37 deletion syndrome",
"pathogenic_variants": [
"Single allele"
]
} | 0.83666 |
co_dise_00168 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in ALB are classified as Pathogenic or Likely Pathogenic for not provided? | NM_000477.7(ALB):c.228_229del (p.Val78fs) VARIANT_IN_GENE ALB -> NM_000477.7(ALB):c.228_229del (p.Val78fs) VARIANT_HAS_CLINICAL_SIGNIFICANCE not provided | {
"steps": [
{
"hop": 1,
"source_node_id": "ALB",
"source_node_type": "GENE",
"source_node_label": "ALB",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000477.7(ALB... | NM_000477.7(ALB):c.1225C>T (p.Gln409Ter); NM_000477.7(ALB):c.70C>T (p.Arg24Ter); NM_000477.7(ALB):c.1020C>A (p.Cys340Ter); NM_000477.7(ALB):c.1378A>T (p.Lys460Ter); NM_000477.7(ALB):c.228_229del (p.Val78fs) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ALB",
"source_db": "UniProt",
"payload": {
"accession": "P02768",
"sequence": "MKWVTFISLLFLFSSAYSRGVFRRDAHKSEVAHRFKDLGEENFKALVLIAFAQYLQQCPFEDHVKLVNEVTEFAKTCVADESAENCDKSLHTLFGDKLCTVATLRETYGEMADCCAKQEPERNECFLQHKDDNPN... | [
{
"source_db": "ClinVar",
"source_id": "NM_000477.7(ALB):c.228_229del (p.Val78fs)",
"text": "NM_000477.7(ALB):c.228_229del (p.Val78fs) VARIANT_IN_GENE ALB",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "DISEASE:not_provided",
"text": "NM_000477.7(ALB):c.228_229del (p.Val... | {
"gene": "ALB",
"disease": "not provided",
"pathogenic_variants": [
"NM_000477.7(ALB):c.1225C>T (p.Gln409Ter)",
"NM_000477.7(ALB):c.70C>T (p.Arg24Ter)",
"NM_000477.7(ALB):c.1020C>A (p.Cys340Ter)",
"NM_000477.7(ALB):c.1378A>T (p.Lys460Ter)",
"NM_000477.7(ALB):c.228_229del (p.Val78fs)",
"NM... | 0.921954 |
co_dise_00169 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in CDK6 are classified as Pathogenic or Likely Pathogenic for microcephaly 12, primary, autosomal recessive? | NM_001145306.2(CDK6):c.589G>A (p.Ala197Thr) VARIANT_IN_GENE CDK6 -> NM_001145306.2(CDK6):c.589G>A (p.Ala197Thr) VARIANT_HAS_CLINICAL_SIGNIFICANCE microcephaly 12, primary, autosomal recessive | {
"steps": [
{
"hop": 1,
"source_node_id": "CDK6",
"source_node_type": "GENE",
"source_node_label": "CDK6",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_001145306.... | NM_001145306.2(CDK6):c.589G>A (p.Ala197Thr) | null | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CDK6",
"source_db": "UniProt",
"payload": {
"accession": "Q00534",
"sequence": "MEKDGLCRADQQYECVAEIGEGAYGKVFKARDLKNGGRFVALKRVRVQTGEEGMPLSTIREVAVLRHLETFEHPNVVRLFDVCTVSRTDRETKLTLVFEHVDQDLTTYLDKVPEPGVPTETIKDMMFQLLRGLD... | [
{
"source_db": "ClinVar",
"source_id": "NM_001145306.2(CDK6):c.589G>A (p.Ala197Thr)",
"text": "NM_001145306.2(CDK6):c.589G>A (p.Ala197Thr) VARIANT_IN_GENE CDK6",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0014484",
"text": "NM_001145306.2(CDK6):c.589G>A (p.Ala19... | {
"gene": "CDK6",
"disease": "microcephaly 12, primary, autosomal recessive",
"pathogenic_variants": [
"NM_001145306.2(CDK6):c.589G>A (p.Ala197Thr)"
]
} | 0.707107 |
co_dise_00170 | disease_reasoning | coding_variant | medium | 2 | According to ClinVar, which variants in BARD1 are classified as Pathogenic or Likely Pathogenic for hereditary breast carcinoma? | NM_000465.4(BARD1):c.601A>T (p.Arg201Ter) VARIANT_IN_GENE BARD1 -> NM_000465.4(BARD1):c.601A>T (p.Arg201Ter) VARIANT_HAS_CLINICAL_SIGNIFICANCE hereditary breast carcinoma | {
"steps": [
{
"hop": 1,
"source_node_id": "BARD1",
"source_node_type": "GENE",
"source_node_label": "BARD1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_db": "ClinVar",
"target_node_id": "NM_000465.4... | NM_000465.4(BARD1):c.1432G>T (p.Glu478Ter); NM_000465.4(BARD1):c.813T>A (p.Cys271Ter); NM_000465.4(BARD1):c.1107del (p.Lys369fs); NM_000465.4(BARD1):c.539del (p.Tyr180fs); NM_000465.4(BARD1):c.7del (p.Asp3fs) | null | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BARD1",
"source_db": "UniProt",
"payload": {
"accession": "Q99728",
"sequence": "MPDNRQPRNRQPRIRSGNEPRSAPAMEPDGRGAWAHSRAALDRLEKLLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQDLKINRQLDSMIQLCSKLRNLLHDNELSDLKEDKPRKSLF... | [
{
"source_db": "ClinVar",
"source_id": "NM_000465.4(BARD1):c.601A>T (p.Arg201Ter)",
"text": "NM_000465.4(BARD1):c.601A>T (p.Arg201Ter) VARIANT_IN_GENE BARD1",
"confidence": 1
},
{
"source_db": "ClinVar",
"source_id": "MONDO:0016419",
"text": "NM_000465.4(BARD1):c.601A>T (p.Arg201Ter)... | {
"gene": "BARD1",
"disease": "hereditary breast carcinoma",
"pathogenic_variants": [
"NM_000465.4(BARD1):c.1432G>T (p.Glu478Ter)",
"NM_000465.4(BARD1):c.813T>A (p.Cys271Ter)",
"NM_000465.4(BARD1):c.1107del (p.Lys369fs)",
"NM_000465.4(BARD1):c.539del (p.Tyr180fs)",
"NM_000465.4(BARD1):c.7del (... | 0.83666 |
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