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_cons_00179 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 17q21.31(chr17:43693538-44212416)x1 (in gene STH), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 17q21.31(chr17:43693538-44212416)x1 VARIANT_IN_GENE STH | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 17q21.31(chr17:43693538-44212416)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 17q21.31(chr17:43693538-44212416)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 17q21.31(chr17:43693538-44212416)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 43693538,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.02954329... | [
{
"source_db": "ClinVar",
"source_id": "STH",
"text": "GRCh37/hg19 17q21.31(chr17:43693538-44212416)x1 VARIANT_IN_GENE STH",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 17q21.31(chr17:43693538-44212416)x1",
"gene": "STH",
"mean_phylop": -0.169,
"track": "phyloP100way"
} | 1 |
co_cons_00180 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 Xp22.33-q28(chrX:2790845-155699618)x3 (in gene LOC130068510), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 Xp22.33-q28(chrX:2790845-155699618)x3 VARIANT_IN_GENE LOC130068510 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 Xp22.33-q28(chrX:2790845-155699618)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 Xp22.33-q28(chrX:2790845-155699618)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 Xp22.33-q28(chrX:2790845-155699618)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chrX",
"pos": 2790845,
"track": "phyloP100way",
"window": 20,
"scores": [
0.212235999... | [
{
"source_db": "ClinVar",
"source_id": "LOC130068510",
"text": "GRCh38/hg38 Xp22.33-q28(chrX:2790845-155699618)x3 VARIANT_IN_GENE LOC130068510",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 Xp22.33-q28(chrX:2790845-155699618)x3",
"gene": "LOC130068510",
"mean_phylop": 0.112,
"track": "phyloP100way"
} | 1 |
co_cons_00181 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_020919.4(ALS2):c.158_160del (p.Gly53del) (in gene ALS2), classify the evolutionary constraint across the variant's genomic window. | NM_020919.4(ALS2):c.158_160del (p.Gly53del) VARIANT_IN_GENE ALS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_020919.4(ALS2):c.158_160del (p.Gly53del)",
"source_node_type": "VARIANT",
"source_node_label": "NM_020919.4(ALS2):c.158_160del (p.Gly53del)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_020919.4(ALS2):c.158_160del (p.Gly53del)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 201767244,
"track": "phyloP100way",
"window": 20,
"scores": [
0.3298500000000... | [
{
"source_db": "ClinVar",
"source_id": "ALS2",
"text": "NM_020919.4(ALS2):c.158_160del (p.Gly53del) VARIANT_IN_GENE ALS2",
"confidence": 1
}
] | {
"variant": "NM_020919.4(ALS2):c.158_160del (p.Gly53del)",
"gene": "ALS2",
"mean_phylop": 3.977,
"track": "phyloP100way"
} | 1 |
co_cons_00182 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 14q32.2-32.33(chr14:96829290-107287663)x1 (in gene IGHE), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 14q32.2-32.33(chr14:96829290-107287663)x1 VARIANT_IN_GENE IGHE | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 14q32.2-32.33(chr14:96829290-107287663)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 14q32.2-32.33(chr14:96829290-107287663)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 14q32.2-32.33(chr14:96829290-107287663)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr14",
"pos": 96829290,
"track": "phyloP100way",
"window": 20,
"scores": [
0.480... | [
{
"source_db": "ClinVar",
"source_id": "IGHE",
"text": "GRCh37/hg19 14q32.2-32.33(chr14:96829290-107287663)x1 VARIANT_IN_GENE IGHE",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 14q32.2-32.33(chr14:96829290-107287663)x1",
"gene": "IGHE",
"mean_phylop": 0.447,
"track": "phyloP100way"
} | 1 |
co_cons_00183 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 12p13.33-11.22(chr12:173786-28219229)x3 (in gene A2M), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 12p13.33-11.22(chr12:173786-28219229)x3 VARIANT_IN_GENE A2M | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 12p13.33-11.22(chr12:173786-28219229)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 12p13.33-11.22(chr12:173786-28219229)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 12p13.33-11.22(chr12:173786-28219229)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr12",
"pos": 173786,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.240276... | [
{
"source_db": "ClinVar",
"source_id": "A2M",
"text": "GRCh37/hg19 12p13.33-11.22(chr12:173786-28219229)x3 VARIANT_IN_GENE A2M",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 12p13.33-11.22(chr12:173786-28219229)x3",
"gene": "A2M",
"mean_phylop": -0.216,
"track": "phyloP100way"
} | 1 |
co_cons_00184 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000055.4(BCHE):c.662del (p.Thr221fs) (in gene BCHE), classify the evolutionary constraint across the variant's genomic window. | NM_000055.4(BCHE):c.662del (p.Thr221fs) VARIANT_IN_GENE BCHE | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000055.4(BCHE):c.662del (p.Thr221fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000055.4(BCHE):c.662del (p.Thr221fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000055.4(BCHE):c.662del (p.Thr221fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 165830372,
"track": "phyloP100way",
"window": 20,
"scores": [
7.77635,
0.... | [
{
"source_db": "ClinVar",
"source_id": "BCHE",
"text": "NM_000055.4(BCHE):c.662del (p.Thr221fs) VARIANT_IN_GENE BCHE",
"confidence": 1
}
] | {
"variant": "NM_000055.4(BCHE):c.662del (p.Thr221fs)",
"gene": "BCHE",
"mean_phylop": 4.11,
"track": "phyloP100way"
} | 1 |
co_cons_00185 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 13q11-34(chr13:19436286-115107733)x3 (in gene ABCC4), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 13q11-34(chr13:19436286-115107733)x3 VARIANT_IN_GENE ABCC4 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 13q11-34(chr13:19436286-115107733)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 13q11-34(chr13:19436286-115107733)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 13q11-34(chr13:19436286-115107733)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr13",
"pos": 19436286,
"track": "phyloP100way",
"window": 20,
"scores": [
0.341134,
... | [
{
"source_db": "ClinVar",
"source_id": "ABCC4",
"text": "GRCh37/hg19 13q11-34(chr13:19436286-115107733)x3 VARIANT_IN_GENE ABCC4",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 13q11-34(chr13:19436286-115107733)x3",
"gene": "ABCC4",
"mean_phylop": 1.343,
"track": "phyloP100way"
} | 1 |
co_cons_00186 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 1p34.3(chr1:35934217-36821999)x4 (in gene ADPRS), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 1p34.3(chr1:35934217-36821999)x4 VARIANT_IN_GENE ADPRS | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 1p34.3(chr1:35934217-36821999)x4",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 1p34.3(chr1:35934217-36821999)x4",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 1p34.3(chr1:35934217-36821999)x4",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 35934217,
"track": "phyloP100way",
"window": 20,
"scores": [
0.911055,
... | [
{
"source_db": "ClinVar",
"source_id": "ADPRS",
"text": "GRCh38/hg38 1p34.3(chr1:35934217-36821999)x4 VARIANT_IN_GENE ADPRS",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 1p34.3(chr1:35934217-36821999)x4",
"gene": "ADPRS",
"mean_phylop": 0.196,
"track": "phyloP100way"
} | 1 |
co_cons_00187 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_003900.5(SQSTM1):c.311_312del (p.Glu104fs) (in gene SQSTM1), classify the evolutionary constraint across the variant's genomic window. | NM_003900.5(SQSTM1):c.311_312del (p.Glu104fs) VARIANT_IN_GENE SQSTM1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_003900.5(SQSTM1):c.311_312del (p.Glu104fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_003900.5(SQSTM1):c.311_312del (p.Glu104fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_003900.5(SQSTM1):c.311_312del (p.Glu104fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr5",
"pos": 179823865,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.5604800000... | [
{
"source_db": "ClinVar",
"source_id": "SQSTM1",
"text": "NM_003900.5(SQSTM1):c.311_312del (p.Glu104fs) VARIANT_IN_GENE SQSTM1",
"confidence": 1
}
] | {
"variant": "NM_003900.5(SQSTM1):c.311_312del (p.Glu104fs)",
"gene": "SQSTM1",
"mean_phylop": 3.047,
"track": "phyloP100way"
} | 1 |
co_cons_00188 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 2p25.3-23.2(chr2:30341-28419664)x3 (in gene LOC126806103), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 2p25.3-23.2(chr2:30341-28419664)x3 VARIANT_IN_GENE LOC126806103 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 2p25.3-23.2(chr2:30341-28419664)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 2p25.3-23.2(chr2:30341-28419664)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 2p25.3-23.2(chr2:30341-28419664)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 30341,
"track": "phyloP100way",
"window": 20,
"scores": [
1.06452,
... | [
{
"source_db": "ClinVar",
"source_id": "LOC126806103",
"text": "GRCh38/hg38 2p25.3-23.2(chr2:30341-28419664)x3 VARIANT_IN_GENE LOC126806103",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 2p25.3-23.2(chr2:30341-28419664)x3",
"gene": "LOC126806103",
"mean_phylop": -0.07200000000000001,
"track": "phyloP100way"
} | 1 |
co_cons_00189 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000044.6(AR):c.1757G>A (p.Arg586Lys) (in gene AR), classify the evolutionary constraint across the variant's genomic window. | NM_000044.6(AR):c.1757G>A (p.Arg586Lys) VARIANT_IN_GENE AR | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000044.6(AR):c.1757G>A (p.Arg586Lys)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000044.6(AR):c.1757G>A (p.Arg586Lys)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000044.6(AR):c.1757G>A (p.Arg586Lys)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chrX",
"pos": 67643396,
"track": "phyloP100way",
"window": 20,
"scores": [
4.7772,
7.79... | [
{
"source_db": "ClinVar",
"source_id": "AR",
"text": "NM_000044.6(AR):c.1757G>A (p.Arg586Lys) VARIANT_IN_GENE AR",
"confidence": 1
}
] | {
"variant": "NM_000044.6(AR):c.1757G>A (p.Arg586Lys)",
"gene": "AR",
"mean_phylop": 5.44,
"track": "phyloP100way"
} | 1 |
co_cons_00190 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_020975.6(RET):c.1998G>C (p.Lys666Asn) (in gene RET), classify the evolutionary constraint across the variant's genomic window. | NM_020975.6(RET):c.1998G>C (p.Lys666Asn) VARIANT_IN_GENE RET | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_020975.6(RET):c.1998G>C (p.Lys666Asn)",
"source_node_type": "VARIANT",
"source_node_label": "NM_020975.6(RET):c.1998G>C (p.Lys666Asn)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_020975.6(RET):c.1998G>C (p.Lys666Asn)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 43114598,
"track": "phyloP100way",
"window": 20,
"scores": [
4.9193,
5.... | [
{
"source_db": "ClinVar",
"source_id": "RET",
"text": "NM_020975.6(RET):c.1998G>C (p.Lys666Asn) VARIANT_IN_GENE RET",
"confidence": 1
}
] | {
"variant": "NM_020975.6(RET):c.1998G>C (p.Lys666Asn)",
"gene": "RET",
"mean_phylop": 3.965,
"track": "phyloP100way"
} | 1 |
co_cons_00191 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 18p11.32-q23(chr18:163323-78005236)x3 (in gene ABHD3), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 18p11.32-q23(chr18:163323-78005236)x3 VARIANT_IN_GENE ABHD3 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 18p11.32-q23(chr18:163323-78005236)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 18p11.32-q23(chr18:163323-78005236)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 18p11.32-q23(chr18:163323-78005236)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr18",
"pos": 163323,
"track": "phyloP100way",
"window": 20,
"scores": [
2.19249,
... | [
{
"source_db": "ClinVar",
"source_id": "ABHD3",
"text": "GRCh37/hg19 18p11.32-q23(chr18:163323-78005236)x3 VARIANT_IN_GENE ABHD3",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 18p11.32-q23(chr18:163323-78005236)x3",
"gene": "ABHD3",
"mean_phylop": 6.449,
"track": "phyloP100way"
} | 1 |
co_cons_00192 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000314.8(PTEN):c.463T>C (p.Tyr155His) (in gene PTEN), classify the evolutionary constraint across the variant's genomic window. | NM_000314.8(PTEN):c.463T>C (p.Tyr155His) VARIANT_IN_GENE PTEN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000314.8(PTEN):c.463T>C (p.Tyr155His)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000314.8(PTEN):c.463T>C (p.Tyr155His)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000314.8(PTEN):c.463T>C (p.Tyr155His)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 87933222,
"track": "phyloP100way",
"window": 20,
"scores": [
7.49076,
2... | [
{
"source_db": "ClinVar",
"source_id": "PTEN",
"text": "NM_000314.8(PTEN):c.463T>C (p.Tyr155His) VARIANT_IN_GENE PTEN",
"confidence": 1
}
] | {
"variant": "NM_000314.8(PTEN):c.463T>C (p.Tyr155His)",
"gene": "PTEN",
"mean_phylop": 6.358,
"track": "phyloP100way"
} | 1 |
co_cons_00193 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 3q25.32-26.31(chr3:158141556-172788324)x3 (in gene LOC129937832), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 3q25.32-26.31(chr3:158141556-172788324)x3 VARIANT_IN_GENE LOC129937832 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 3q25.32-26.31(chr3:158141556-172788324)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 3q25.32-26.31(chr3:158141556-172788324)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 3q25.32-26.31(chr3:158141556-172788324)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 158141556,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.82... | [
{
"source_db": "ClinVar",
"source_id": "LOC129937832",
"text": "GRCh38/hg38 3q25.32-26.31(chr3:158141556-172788324)x3 VARIANT_IN_GENE LOC129937832",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 3q25.32-26.31(chr3:158141556-172788324)x3",
"gene": "LOC129937832",
"mean_phylop": -0.026000000000000002,
"track": "phyloP100way"
} | 1 |
co_cons_00194 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 13q11-34(chr13:18445862-114327173)x1 (in gene LOC130009931), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 13q11-34(chr13:18445862-114327173)x1 VARIANT_IN_GENE LOC130009931 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 13q11-34(chr13:18445862-114327173)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 13q11-34(chr13:18445862-114327173)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 13q11-34(chr13:18445862-114327173)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr13",
"pos": 18445862,
"track": "phyloP100way",
"window": 20,
"scores": [
0.11378,
... | [
{
"source_db": "ClinVar",
"source_id": "LOC130009931",
"text": "GRCh38/hg38 13q11-34(chr13:18445862-114327173)x1 VARIANT_IN_GENE LOC130009931",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 13q11-34(chr13:18445862-114327173)x1",
"gene": "LOC130009931",
"mean_phylop": -0.069,
"track": "phyloP100way"
} | 1 |
co_cons_00195 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 20p13-11.1(chr20:80927-26324843)x3 (in gene LOC130065565), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 20p13-11.1(chr20:80927-26324843)x3 VARIANT_IN_GENE LOC130065565 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 20p13-11.1(chr20:80927-26324843)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 20p13-11.1(chr20:80927-26324843)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 20p13-11.1(chr20:80927-26324843)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr20",
"pos": 80927,
"track": "phyloP100way",
"window": 20,
"scores": [
0.179835,
... | [
{
"source_db": "ClinVar",
"source_id": "LOC130065565",
"text": "GRCh38/hg38 20p13-11.1(chr20:80927-26324843)x3 VARIANT_IN_GENE LOC130065565",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 20p13-11.1(chr20:80927-26324843)x3",
"gene": "LOC130065565",
"mean_phylop": 0.098,
"track": "phyloP100way"
} | 1 |
co_cons_00196 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_004360.5(CDH1):c.940A>T (p.Lys314Ter) (in gene CDH1), classify the evolutionary constraint across the variant's genomic window. | NM_004360.5(CDH1):c.940A>T (p.Lys314Ter) VARIANT_IN_GENE CDH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004360.5(CDH1):c.940A>T (p.Lys314Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004360.5(CDH1):c.940A>T (p.Lys314Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_004360.5(CDH1):c.940A>T (p.Lys314Ter)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr16",
"pos": 68811791,
"track": "phyloP100way",
"window": 20,
"scores": [
8.86197,
0... | [
{
"source_db": "ClinVar",
"source_id": "CDH1",
"text": "NM_004360.5(CDH1):c.940A>T (p.Lys314Ter) VARIANT_IN_GENE CDH1",
"confidence": 1
}
] | {
"variant": "NM_004360.5(CDH1):c.940A>T (p.Lys314Ter)",
"gene": "CDH1",
"mean_phylop": 2.117,
"track": "phyloP100way"
} | 1 |
co_cons_00197 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 16p13.3(chr16:3726702-4644961)x3 (in gene ADCY9), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 16p13.3(chr16:3726702-4644961)x3 VARIANT_IN_GENE ADCY9 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 16p13.3(chr16:3726702-4644961)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 16p13.3(chr16:3726702-4644961)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 16p13.3(chr16:3726702-4644961)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr16",
"pos": 3726702,
"track": "phyloP100way",
"window": 20,
"scores": [
5.45073,
... | [
{
"source_db": "ClinVar",
"source_id": "ADCY9",
"text": "GRCh38/hg38 16p13.3(chr16:3726702-4644961)x3 VARIANT_IN_GENE ADCY9",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 16p13.3(chr16:3726702-4644961)x3",
"gene": "ADCY9",
"mean_phylop": 4.029,
"track": "phyloP100way"
} | 1 |
co_cons_00198 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 10q25.1-26.3(chr10:106003533-135427143)x3 (in gene ABLIM1), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 10q25.1-26.3(chr10:106003533-135427143)x3 VARIANT_IN_GENE ABLIM1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 10q25.1-26.3(chr10:106003533-135427143)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 10q25.1-26.3(chr10:106003533-135427143)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 10q25.1-26.3(chr10:106003533-135427143)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 106003533,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.9... | [
{
"source_db": "ClinVar",
"source_id": "ABLIM1",
"text": "GRCh37/hg19 10q25.1-26.3(chr10:106003533-135427143)x3 VARIANT_IN_GENE ABLIM1",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 10q25.1-26.3(chr10:106003533-135427143)x3",
"gene": "ABLIM1",
"mean_phylop": -0.28800000000000003,
"track": "phyloP100way"
} | 1 |
co_cons_00199 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 7p21.3-21.2(chr7:11122492-16479303)x1 (in gene AGMO), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 7p21.3-21.2(chr7:11122492-16479303)x1 VARIANT_IN_GENE AGMO | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 7p21.3-21.2(chr7:11122492-16479303)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 7p21.3-21.2(chr7:11122492-16479303)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 7p21.3-21.2(chr7:11122492-16479303)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 11122492,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.679157,... | [
{
"source_db": "ClinVar",
"source_id": "AGMO",
"text": "GRCh38/hg38 7p21.3-21.2(chr7:11122492-16479303)x1 VARIANT_IN_GENE AGMO",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 7p21.3-21.2(chr7:11122492-16479303)x1",
"gene": "AGMO",
"mean_phylop": 0.232,
"track": "phyloP100way"
} | 1 |
co_cons_00200 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 2p25.3-22.3(chr2:12770-33711509)x3 (in gene ABHD1), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 2p25.3-22.3(chr2:12770-33711509)x3 VARIANT_IN_GENE ABHD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 2p25.3-22.3(chr2:12770-33711509)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 2p25.3-22.3(chr2:12770-33711509)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 2p25.3-22.3(chr2:12770-33711509)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 12770,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.6402909999999... | [
{
"source_db": "ClinVar",
"source_id": "ABHD1",
"text": "GRCh38/hg38 2p25.3-22.3(chr2:12770-33711509)x3 VARIANT_IN_GENE ABHD1",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 2p25.3-22.3(chr2:12770-33711509)x3",
"gene": "ABHD1",
"mean_phylop": -0.164,
"track": "phyloP100way"
} | 1 |
co_cons_00201 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 22q11.23(chr22:23698818-25042987)x3 (in gene ADORA2A), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 22q11.23(chr22:23698818-25042987)x3 VARIANT_IN_GENE ADORA2A | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 22q11.23(chr22:23698818-25042987)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 22q11.23(chr22:23698818-25042987)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 22q11.23(chr22:23698818-25042987)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr22",
"pos": 23698818,
"track": "phyloP100way",
"window": 20,
"scores": [
0.761685,
... | [
{
"source_db": "ClinVar",
"source_id": "ADORA2A",
"text": "GRCh37/hg19 22q11.23(chr22:23698818-25042987)x3 VARIANT_IN_GENE ADORA2A",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 22q11.23(chr22:23698818-25042987)x3",
"gene": "ADORA2A",
"mean_phylop": 0.502,
"track": "phyloP100way"
} | 1 |
co_cons_00202 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly) (in gene TARDBP), classify the evolutionary constraint across the variant's genomic window. | NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly) VARIANT_IN_GENE TARDBP | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 11018836,
"track": "phyloP100way",
"window": 20,
"scores": [
4.10895,
... | [
{
"source_db": "ClinVar",
"source_id": "TARDBP",
"text": "NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly) VARIANT_IN_GENE TARDBP",
"confidence": 1
}
] | {
"variant": "NM_007375.4(TARDBP):c.506A>G (p.Asp169Gly)",
"gene": "TARDBP",
"mean_phylop": 6.203,
"track": "phyloP100way"
} | 1 |
co_cons_00203 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000484.4(APP):c.2155A>C (p.Thr719Pro) (in gene APP), classify the evolutionary constraint across the variant's genomic window. | NM_000484.4(APP):c.2155A>C (p.Thr719Pro) VARIANT_IN_GENE APP | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000484.4(APP):c.2155A>C (p.Thr719Pro)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000484.4(APP):c.2155A>C (p.Thr719Pro)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000484.4(APP):c.2155A>C (p.Thr719Pro)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr21",
"pos": 25891778,
"track": "phyloP100way",
"window": 20,
"scores": [
4.65458,
7... | [
{
"source_db": "ClinVar",
"source_id": "APP",
"text": "NM_000484.4(APP):c.2155A>C (p.Thr719Pro) VARIANT_IN_GENE APP",
"confidence": 1
}
] | {
"variant": "NM_000484.4(APP):c.2155A>C (p.Thr719Pro)",
"gene": "APP",
"mean_phylop": 5.79,
"track": "phyloP100way"
} | 1 |
co_cons_00204 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3 (in gene LOC130061427), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3 VARIANT_IN_GENE LOC130061427 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 36449220,
"track": "phyloP100way",
"window": 20,
"scores": [
0.1427... | [
{
"source_db": "ClinVar",
"source_id": "LOC130061427",
"text": "GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3 VARIANT_IN_GENE LOC130061427",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 17q21.33-24.2(chr17:36449220-68170214)x3",
"gene": "LOC130061427",
"mean_phylop": -0.013000000000000001,
"track": "phyloP100way"
} | 1 |
co_cons_00205 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 1p36.23-36.21(chr1:8255222-12785220)x3 (in gene AADACL3), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 1p36.23-36.21(chr1:8255222-12785220)x3 VARIANT_IN_GENE AADACL3 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 1p36.23-36.21(chr1:8255222-12785220)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 1p36.23-36.21(chr1:8255222-12785220)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 1p36.23-36.21(chr1:8255222-12785220)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 8255222,
"track": "phyloP100way",
"window": 20,
"scores": [
0.120835,
... | [
{
"source_db": "ClinVar",
"source_id": "AADACL3",
"text": "GRCh37/hg19 1p36.23-36.21(chr1:8255222-12785220)x3 VARIANT_IN_GENE AADACL3",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 1p36.23-36.21(chr1:8255222-12785220)x3",
"gene": "AADACL3",
"mean_phylop": -0.113,
"track": "phyloP100way"
} | 1 |
co_cons_00206 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000059.4(BRCA2):c.8024_8025del (p.Ile2675fs) (in gene BRCA2), classify the evolutionary constraint across the variant's genomic window. | NM_000059.4(BRCA2):c.8024_8025del (p.Ile2675fs) VARIANT_IN_GENE BRCA2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000059.4(BRCA2):c.8024_8025del (p.Ile2675fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000059.4(BRCA2):c.8024_8025del (p.Ile2675fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000059.4(BRCA2):c.8024_8025del (p.Ile2675fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr13",
"pos": 32363225,
"track": "phyloP100way",
"window": 20,
"scores": [
1.59016,
... | [
{
"source_db": "ClinVar",
"source_id": "BRCA2",
"text": "NM_000059.4(BRCA2):c.8024_8025del (p.Ile2675fs) VARIANT_IN_GENE BRCA2",
"confidence": 1
}
] | {
"variant": "NM_000059.4(BRCA2):c.8024_8025del (p.Ile2675fs)",
"gene": "BRCA2",
"mean_phylop": 4.206,
"track": "phyloP100way"
} | 1 |
co_cons_00207 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_002878.4(RAD51D):c.580_583dup (p.Gly195fs) (in gene RAD51D), classify the evolutionary constraint across the variant's genomic window. | NM_002878.4(RAD51D):c.580_583dup (p.Gly195fs) VARIANT_IN_GENE RAD51D | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_002878.4(RAD51D):c.580_583dup (p.Gly195fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_002878.4(RAD51D):c.580_583dup (p.Gly195fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_002878.4(RAD51D):c.580_583dup (p.Gly195fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 35103537,
"track": "phyloP100way",
"window": 20,
"scores": [
0.657906,
... | [
{
"source_db": "ClinVar",
"source_id": "RAD51D",
"text": "NM_002878.4(RAD51D):c.580_583dup (p.Gly195fs) VARIANT_IN_GENE RAD51D",
"confidence": 1
}
] | {
"variant": "NM_002878.4(RAD51D):c.580_583dup (p.Gly195fs)",
"gene": "RAD51D",
"mean_phylop": 0.75,
"track": "phyloP100way"
} | 1 |
co_cons_00208 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_007294.4(BRCA1):c.3866del (p.Thr1289fs) (in gene BRCA1), classify the evolutionary constraint across the variant's genomic window. | NM_007294.4(BRCA1):c.3866del (p.Thr1289fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.3866del (p.Thr1289fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.3866del (p.Thr1289fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"intercell_role",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_007294.4(BRCA1):c.3866del (p.Thr1289fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 43091665,
"track": "phyloP100way",
"window": 20,
"scores": [
5.76972,
... | [
{
"source_db": "ClinVar",
"source_id": "BRCA1",
"text": "NM_007294.4(BRCA1):c.3866del (p.Thr1289fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.3866del (p.Thr1289fs)",
"gene": "BRCA1",
"mean_phylop": 1.216,
"track": "phyloP100way"
} | 1 |
co_cons_00209 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 7q22.1-31.31(chr7:100676872-119156160) (in gene ORAI2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 7q22.1-31.31(chr7:100676872-119156160) VARIANT_IN_GENE ORAI2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 7q22.1-31.31(chr7:100676872-119156160)",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 7q22.1-31.31(chr7:100676872-119156160)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 7q22.1-31.31(chr7:100676872-119156160)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 100676872,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.96455... | [
{
"source_db": "ClinVar",
"source_id": "ORAI2",
"text": "GRCh37/hg19 7q22.1-31.31(chr7:100676872-119156160) VARIANT_IN_GENE ORAI2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 7q22.1-31.31(chr7:100676872-119156160)",
"gene": "ORAI2",
"mean_phylop": -1.011,
"track": "phyloP100way"
} | 1 |
co_cons_00210 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001904.4(CTNNB1):c.1690dup (p.Val564fs) (in gene CTNNB1), classify the evolutionary constraint across the variant's genomic window. | NM_001904.4(CTNNB1):c.1690dup (p.Val564fs) VARIANT_IN_GENE CTNNB1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001904.4(CTNNB1):c.1690dup (p.Val564fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001904.4(CTNNB1):c.1690dup (p.Val564fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001904.4(CTNNB1):c.1690dup (p.Val564fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 41235725,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.390953,
... | [
{
"source_db": "ClinVar",
"source_id": "CTNNB1",
"text": "NM_001904.4(CTNNB1):c.1690dup (p.Val564fs) VARIANT_IN_GENE CTNNB1",
"confidence": 1
}
] | {
"variant": "NM_001904.4(CTNNB1):c.1690dup (p.Val564fs)",
"gene": "CTNNB1",
"mean_phylop": 3.885,
"track": "phyloP100way"
} | 1 |
co_cons_00211 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000002.11:g.(?_47656871)_(47698211_?)dup (in gene MSH2), classify the evolutionary constraint across the variant's genomic window. | NC_000002.11:g.(?_47656871)_(47698211_?)dup VARIANT_IN_GENE MSH2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000002.11:g.(?_47656871)_(47698211_?)dup",
"source_node_type": "VARIANT",
"source_node_label": "NC_000002.11:g.(?_47656871)_(47698211_?)dup",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NC_000002.11:g.(?_47656871)_(47698211_?)dup",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 47656871,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.921528,
... | [
{
"source_db": "ClinVar",
"source_id": "MSH2",
"text": "NC_000002.11:g.(?_47656871)_(47698211_?)dup VARIANT_IN_GENE MSH2",
"confidence": 1
}
] | {
"variant": "NC_000002.11:g.(?_47656871)_(47698211_?)dup",
"gene": "MSH2",
"mean_phylop": -0.051000000000000004,
"track": "phyloP100way"
} | 1 |
co_cons_00212 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_003106.4(SOX2):c.582_583delinsTT (p.Met194_Gln195delinsIleTer) (in gene SOX2-OT), classify the evolutionary constraint across the variant's genomic window. | NM_003106.4(SOX2):c.582_583delinsTT (p.Met194_Gln195delinsIleTer) VARIANT_IN_GENE SOX2-OT | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_003106.4(SOX2):c.582_583delinsTT (p.Met194_Gln195delinsIleTer)",
"source_node_type": "VARIANT",
"source_node_label": "NM_003106.4(SOX2):c.582_583delinsTT (p.Met194_Gln195delinsIleTer)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evi... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_003106.4(SOX2):c.582_583delinsTT (p.Met194_Gln195delinsIleTer)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 181712942,
"track": "phyloP100way",
"window": 20,
"scores": [
... | [
{
"source_db": "ClinVar",
"source_id": "SOX2-OT",
"text": "NM_003106.4(SOX2):c.582_583delinsTT (p.Met194_Gln195delinsIleTer) VARIANT_IN_GENE SOX2-OT",
"confidence": 1
}
] | {
"variant": "NM_003106.4(SOX2):c.582_583delinsTT (p.Met194_Gln195delinsIleTer)",
"gene": "SOX2-OT",
"mean_phylop": 5.329,
"track": "phyloP100way"
} | 1 |
co_cons_00213 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 7p13-12.2(chr7:43341583-50171623) (in gene MRPS24), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 7p13-12.2(chr7:43341583-50171623) VARIANT_IN_GENE MRPS24 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 7p13-12.2(chr7:43341583-50171623)",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 7p13-12.2(chr7:43341583-50171623)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 7p13-12.2(chr7:43341583-50171623)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr7",
"pos": 43341583,
"track": "phyloP100way",
"window": 20,
"scores": [
0.249024,
... | [
{
"source_db": "ClinVar",
"source_id": "MRPS24",
"text": "GRCh37/hg19 7p13-12.2(chr7:43341583-50171623) VARIANT_IN_GENE MRPS24",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 7p13-12.2(chr7:43341583-50171623)",
"gene": "MRPS24",
"mean_phylop": 0.212,
"track": "phyloP100way"
} | 1 |
co_cons_00214 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 2q35-36.3(chr2:220056891-227164817)x1 (in gene ABCB6), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 2q35-36.3(chr2:220056891-227164817)x1 VARIANT_IN_GENE ABCB6 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 2q35-36.3(chr2:220056891-227164817)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 2q35-36.3(chr2:220056891-227164817)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 2q35-36.3(chr2:220056891-227164817)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 220056891,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.634953... | [
{
"source_db": "ClinVar",
"source_id": "ABCB6",
"text": "GRCh37/hg19 2q35-36.3(chr2:220056891-227164817)x1 VARIANT_IN_GENE ABCB6",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 2q35-36.3(chr2:220056891-227164817)x1",
"gene": "ABCB6",
"mean_phylop": -0.112,
"track": "phyloP100way"
} | 1 |
co_cons_00215 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 4p16.3-15.33(chr4:72555-12898612)x1 (in gene ABLIM2), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 4p16.3-15.33(chr4:72555-12898612)x1 VARIANT_IN_GENE ABLIM2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 4p16.3-15.33(chr4:72555-12898612)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 4p16.3-15.33(chr4:72555-12898612)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 4p16.3-15.33(chr4:72555-12898612)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 72555,
"track": "phyloP100way",
"window": 20,
"scores": [
0.314197,
... | [
{
"source_db": "ClinVar",
"source_id": "ABLIM2",
"text": "GRCh38/hg38 4p16.3-15.33(chr4:72555-12898612)x1 VARIANT_IN_GENE ABLIM2",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 4p16.3-15.33(chr4:72555-12898612)x1",
"gene": "ABLIM2",
"mean_phylop": 0.14300000000000002,
"track": "phyloP100way"
} | 1 |
co_cons_00216 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 10p15.1-13(chr10:4802753-16823491)x1 (in gene LOC130003418), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 10p15.1-13(chr10:4802753-16823491)x1 VARIANT_IN_GENE LOC130003418 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 10p15.1-13(chr10:4802753-16823491)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 10p15.1-13(chr10:4802753-16823491)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 10p15.1-13(chr10:4802753-16823491)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 4802753,
"track": "phyloP100way",
"window": 20,
"scores": [
1.31756,
... | [
{
"source_db": "ClinVar",
"source_id": "LOC130003418",
"text": "GRCh38/hg38 10p15.1-13(chr10:4802753-16823491)x1 VARIANT_IN_GENE LOC130003418",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 10p15.1-13(chr10:4802753-16823491)x1",
"gene": "LOC130003418",
"mean_phylop": 0.263,
"track": "phyloP100way"
} | 1 |
co_cons_00217 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001256864.2(DNAJC6):c.2456dup (p.Gln820fs) (in gene DNAJC6), classify the evolutionary constraint across the variant's genomic window. | NM_001256864.2(DNAJC6):c.2456dup (p.Gln820fs) VARIANT_IN_GENE DNAJC6 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001256864.2(DNAJC6):c.2456dup (p.Gln820fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001256864.2(DNAJC6):c.2456dup (p.Gln820fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001256864.2(DNAJC6):c.2456dup (p.Gln820fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 65406093,
"track": "phyloP100way",
"window": 20,
"scores": [
7.32851,
... | [
{
"source_db": "ClinVar",
"source_id": "DNAJC6",
"text": "NM_001256864.2(DNAJC6):c.2456dup (p.Gln820fs) VARIANT_IN_GENE DNAJC6",
"confidence": 1
}
] | {
"variant": "NM_001256864.2(DNAJC6):c.2456dup (p.Gln820fs)",
"gene": "DNAJC6",
"mean_phylop": 3.195,
"track": "phyloP100way"
} | 1 |
co_cons_00218 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 2q35-37.3(chr2:215591606-239217386)x3 (in gene AAMP), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 2q35-37.3(chr2:215591606-239217386)x3 VARIANT_IN_GENE AAMP | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 2q35-37.3(chr2:215591606-239217386)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 2q35-37.3(chr2:215591606-239217386)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | A | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 2q35-37.3(chr2:215591606-239217386)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 215591606,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.089393... | [
{
"source_db": "ClinVar",
"source_id": "AAMP",
"text": "GRCh37/hg19 2q35-37.3(chr2:215591606-239217386)x3 VARIANT_IN_GENE AAMP",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 2q35-37.3(chr2:215591606-239217386)x3",
"gene": "AAMP",
"mean_phylop": -0.309,
"track": "phyloP100way"
} | 1 |
co_cons_00219 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000051.4(ATM):c.2410del (p.Leu804fs) (in gene ATM), classify the evolutionary constraint across the variant's genomic window. | NM_000051.4(ATM):c.2410del (p.Leu804fs) VARIANT_IN_GENE ATM | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000051.4(ATM):c.2410del (p.Leu804fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000051.4(ATM):c.2410del (p.Leu804fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000051.4(ATM):c.2410del (p.Leu804fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr11",
"pos": 108259018,
"track": "phyloP100way",
"window": 20,
"scores": [
4.51842,
4... | [
{
"source_db": "ClinVar",
"source_id": "ATM",
"text": "NM_000051.4(ATM):c.2410del (p.Leu804fs) VARIANT_IN_GENE ATM",
"confidence": 1
}
] | {
"variant": "NM_000051.4(ATM):c.2410del (p.Leu804fs)",
"gene": "ATM",
"mean_phylop": 2.458,
"track": "phyloP100way"
} | 1 |
co_cons_00220 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 4q35.1-35.2(chr4:184648532-190957473)x1 (in gene ACSL1), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 4q35.1-35.2(chr4:184648532-190957473)x1 VARIANT_IN_GENE ACSL1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 4q35.1-35.2(chr4:184648532-190957473)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 4q35.1-35.2(chr4:184648532-190957473)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 4q35.1-35.2(chr4:184648532-190957473)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 184648532,
"track": "phyloP100way",
"window": 20,
"scores": [
0.06688... | [
{
"source_db": "ClinVar",
"source_id": "ACSL1",
"text": "GRCh37/hg19 4q35.1-35.2(chr4:184648532-190957473)x1 VARIANT_IN_GENE ACSL1",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 4q35.1-35.2(chr4:184648532-190957473)x1",
"gene": "ACSL1",
"mean_phylop": -0.419,
"track": "phyloP100way"
} | 1 |
co_cons_00221 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000011.9:g.(?_111171709)_(111958707_?)del (in gene DIXDC1), classify the evolutionary constraint across the variant's genomic window. | NC_000011.9:g.(?_111171709)_(111958707_?)del VARIANT_IN_GENE DIXDC1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000011.9:g.(?_111171709)_(111958707_?)del",
"source_node_type": "VARIANT",
"source_node_label": "NC_000011.9:g.(?_111171709)_(111958707_?)del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | A | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NC_000011.9:g.(?_111171709)_(111958707_?)del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr11",
"pos": 111171709,
"track": "phyloP100way",
"window": 20,
"scores": [
0.0508189,
... | [
{
"source_db": "ClinVar",
"source_id": "DIXDC1",
"text": "NC_000011.9:g.(?_111171709)_(111958707_?)del VARIANT_IN_GENE DIXDC1",
"confidence": 1
}
] | {
"variant": "NC_000011.9:g.(?_111171709)_(111958707_?)del",
"gene": "DIXDC1",
"mean_phylop": -0.125,
"track": "phyloP100way"
} | 1 |
co_cons_00222 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 3q26.1-26.33(chr3:165158611-180130168)x3 (in gene ACTL6A), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 3q26.1-26.33(chr3:165158611-180130168)x3 VARIANT_IN_GENE ACTL6A | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 3q26.1-26.33(chr3:165158611-180130168)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 3q26.1-26.33(chr3:165158611-180130168)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 3q26.1-26.33(chr3:165158611-180130168)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 165158611,
"track": "phyloP100way",
"window": 20,
"scores": [
0.0670... | [
{
"source_db": "ClinVar",
"source_id": "ACTL6A",
"text": "GRCh38/hg38 3q26.1-26.33(chr3:165158611-180130168)x3 VARIANT_IN_GENE ACTL6A",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 3q26.1-26.33(chr3:165158611-180130168)x3",
"gene": "ACTL6A",
"mean_phylop": -0.114,
"track": "phyloP100way"
} | 1 |
co_cons_00223 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 8p23.1-11.22(chr8:12560782-38748763)x3 (in gene ADAM28), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 8p23.1-11.22(chr8:12560782-38748763)x3 VARIANT_IN_GENE ADAM28 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 8p23.1-11.22(chr8:12560782-38748763)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 8p23.1-11.22(chr8:12560782-38748763)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 8p23.1-11.22(chr8:12560782-38748763)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr8",
"pos": 12560782,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.788690... | [
{
"source_db": "ClinVar",
"source_id": "ADAM28",
"text": "GRCh37/hg19 8p23.1-11.22(chr8:12560782-38748763)x3 VARIANT_IN_GENE ADAM28",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 8p23.1-11.22(chr8:12560782-38748763)x3",
"gene": "ADAM28",
"mean_phylop": -0.5720000000000001,
"track": "phyloP100way"
} | 1 |
co_cons_00224 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000003.11:g.(?_37034542)_(37035260_?)del (in gene EPM2AIP1), classify the evolutionary constraint across the variant's genomic window. | NC_000003.11:g.(?_37034542)_(37035260_?)del VARIANT_IN_GENE EPM2AIP1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000003.11:g.(?_37034542)_(37035260_?)del",
"source_node_type": "VARIANT",
"source_node_label": "NC_000003.11:g.(?_37034542)_(37035260_?)del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NC_000003.11:g.(?_37034542)_(37035260_?)del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr3",
"pos": 37034542,
"track": "phyloP100way",
"window": 20,
"scores": [
0.317575,
... | [
{
"source_db": "ClinVar",
"source_id": "EPM2AIP1",
"text": "NC_000003.11:g.(?_37034542)_(37035260_?)del VARIANT_IN_GENE EPM2AIP1",
"confidence": 1
}
] | {
"variant": "NC_000003.11:g.(?_37034542)_(37035260_?)del",
"gene": "EPM2AIP1",
"mean_phylop": 0.028,
"track": "phyloP100way"
} | 1 |
co_cons_00225 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 10q26.3(chr10:131914873-133613938)x1 (in gene ADAM8), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 10q26.3(chr10:131914873-133613938)x1 VARIANT_IN_GENE ADAM8 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 10q26.3(chr10:131914873-133613938)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 10q26.3(chr10:131914873-133613938)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 10q26.3(chr10:131914873-133613938)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr10",
"pos": 131914873,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.887299... | [
{
"source_db": "ClinVar",
"source_id": "ADAM8",
"text": "GRCh38/hg38 10q26.3(chr10:131914873-133613938)x1 VARIANT_IN_GENE ADAM8",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 10q26.3(chr10:131914873-133613938)x1",
"gene": "ADAM8",
"mean_phylop": -0.502,
"track": "phyloP100way"
} | 1 |
co_cons_00226 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_007294.4(BRCA1):c.3997del (p.Val1333fs) (in gene LOC126862571), classify the evolutionary constraint across the variant's genomic window. | NM_007294.4(BRCA1):c.3997del (p.Val1333fs) VARIANT_IN_GENE LOC126862571 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.3997del (p.Val1333fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.3997del (p.Val1333fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_007294.4(BRCA1):c.3997del (p.Val1333fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 43091534,
"track": "phyloP100way",
"window": 20,
"scores": [
0.371646,
... | [
{
"source_db": "ClinVar",
"source_id": "LOC126862571",
"text": "NM_007294.4(BRCA1):c.3997del (p.Val1333fs) VARIANT_IN_GENE LOC126862571",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.3997del (p.Val1333fs)",
"gene": "LOC126862571",
"mean_phylop": 0.372,
"track": "phyloP100way"
} | 1 |
co_cons_00227 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001291303.3(FAT4):c.14610del (p.Lys4871fs) (in gene FAT4), classify the evolutionary constraint across the variant's genomic window. | NM_001291303.3(FAT4):c.14610del (p.Lys4871fs) VARIANT_IN_GENE FAT4 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001291303.3(FAT4):c.14610del (p.Lys4871fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001291303.3(FAT4):c.14610del (p.Lys4871fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001291303.3(FAT4):c.14610del (p.Lys4871fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 125491424,
"track": "phyloP100way",
"window": 20,
"scores": [
3.82247,
... | [
{
"source_db": "ClinVar",
"source_id": "FAT4",
"text": "NM_001291303.3(FAT4):c.14610del (p.Lys4871fs) VARIANT_IN_GENE FAT4",
"confidence": 1
}
] | {
"variant": "NM_001291303.3(FAT4):c.14610del (p.Lys4871fs)",
"gene": "FAT4",
"mean_phylop": 3.8689999999999998,
"track": "phyloP100way"
} | 1 |
co_cons_00228 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 17q22(chr17:52189051-57477162)x3 (in gene HSF5), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 17q22(chr17:52189051-57477162)x3 VARIANT_IN_GENE HSF5 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 17q22(chr17:52189051-57477162)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 17q22(chr17:52189051-57477162)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 17q22(chr17:52189051-57477162)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 52189051,
"track": "phyloP100way",
"window": 20,
"scores": [
0.534323,
... | [
{
"source_db": "ClinVar",
"source_id": "HSF5",
"text": "GRCh37/hg19 17q22(chr17:52189051-57477162)x3 VARIANT_IN_GENE HSF5",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 17q22(chr17:52189051-57477162)x3",
"gene": "HSF5",
"mean_phylop": 0.117,
"track": "phyloP100way"
} | 1 |
co_cons_00229 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_004119.3(FLT3):c.2503G>C (p.Asp835His) (in gene FLT3), classify the evolutionary constraint across the variant's genomic window. | NM_004119.3(FLT3):c.2503G>C (p.Asp835His) VARIANT_IN_GENE FLT3 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004119.3(FLT3):c.2503G>C (p.Asp835His)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004119.3(FLT3):c.2503G>C (p.Asp835His)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_004119.3(FLT3):c.2503G>C (p.Asp835His)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr13",
"pos": 28018505,
"track": "phyloP100way",
"window": 20,
"scores": [
4.796110000000000... | [
{
"source_db": "ClinVar",
"source_id": "FLT3",
"text": "NM_004119.3(FLT3):c.2503G>C (p.Asp835His) VARIANT_IN_GENE FLT3",
"confidence": 1
}
] | {
"variant": "NM_004119.3(FLT3):c.2503G>C (p.Asp835His)",
"gene": "FLT3",
"mean_phylop": 4.514,
"track": "phyloP100way"
} | 1 |
co_cons_00230 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000454.5(SOD1):c.338T>C (p.Ile113Thr) (in gene SOD1), classify the evolutionary constraint across the variant's genomic window. | NM_000454.5(SOD1):c.338T>C (p.Ile113Thr) VARIANT_IN_GENE SOD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000454.5(SOD1):c.338T>C (p.Ile113Thr)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000454.5(SOD1):c.338T>C (p.Ile113Thr)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000454.5(SOD1):c.338T>C (p.Ile113Thr)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr21",
"pos": 31667356,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.53198,
... | [
{
"source_db": "ClinVar",
"source_id": "SOD1",
"text": "NM_000454.5(SOD1):c.338T>C (p.Ile113Thr) VARIANT_IN_GENE SOD1",
"confidence": 1
}
] | {
"variant": "NM_000454.5(SOD1):c.338T>C (p.Ile113Thr)",
"gene": "SOD1",
"mean_phylop": 3.456,
"track": "phyloP100way"
} | 1 |
co_cons_00231 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 20p13-12.3(chr20:2463101-8185680)x1 (in gene ADAM33), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 20p13-12.3(chr20:2463101-8185680)x1 VARIANT_IN_GENE ADAM33 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 20p13-12.3(chr20:2463101-8185680)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 20p13-12.3(chr20:2463101-8185680)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | C | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 20p13-12.3(chr20:2463101-8185680)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr20",
"pos": 2463101,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.15562,
... | [
{
"source_db": "ClinVar",
"source_id": "ADAM33",
"text": "GRCh37/hg19 20p13-12.3(chr20:2463101-8185680)x1 VARIANT_IN_GENE ADAM33",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 20p13-12.3(chr20:2463101-8185680)x1",
"gene": "ADAM33",
"mean_phylop": 4.991,
"track": "phyloP100way"
} | 1 |
co_cons_00232 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000019.9:g.(?_852323)_(1226652_?)del (in gene ARID3A), classify the evolutionary constraint across the variant's genomic window. | NC_000019.9:g.(?_852323)_(1226652_?)del VARIANT_IN_GENE ARID3A | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000019.9:g.(?_852323)_(1226652_?)del",
"source_node_type": "VARIANT",
"source_node_label": "NC_000019.9:g.(?_852323)_(1226652_?)del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NC_000019.9:g.(?_852323)_(1226652_?)del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr19",
"pos": 852323,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.06031,
0.2... | [
{
"source_db": "ClinVar",
"source_id": "ARID3A",
"text": "NC_000019.9:g.(?_852323)_(1226652_?)del VARIANT_IN_GENE ARID3A",
"confidence": 1
}
] | {
"variant": "NC_000019.9:g.(?_852323)_(1226652_?)del",
"gene": "ARID3A",
"mean_phylop": -0.453,
"track": "phyloP100way"
} | 1 |
co_cons_00233 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000006.11:g.(162683798_162864341)_(162864506_163148693)dup (in gene PACRG), classify the evolutionary constraint across the variant's genomic window. | NC_000006.11:g.(162683798_162864341)_(162864506_163148693)dup VARIANT_IN_GENE PACRG | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000006.11:g.(162683798_162864341)_(162864506_163148693)dup",
"source_node_type": "VARIANT",
"source_node_label": "NC_000006.11:g.(162683798_162864341)_(162864506_163148693)dup",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_ty... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NC_000006.11:g.(162683798_162864341)_(162864506_163148693)dup",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr6",
"pos": 162683798,
"track": "phyloP100way",
"window": 20,
"scores": [
... | [
{
"source_db": "ClinVar",
"source_id": "PACRG",
"text": "NC_000006.11:g.(162683798_162864341)_(162864506_163148693)dup VARIANT_IN_GENE PACRG",
"confidence": 1
}
] | {
"variant": "NC_000006.11:g.(162683798_162864341)_(162864506_163148693)dup",
"gene": "PACRG",
"mean_phylop": 0.215,
"track": "phyloP100way"
} | 1 |
co_cons_00234 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000077.5(CDKN2A):c.381_393delinsGATGCG (p.Arg128fs) (in gene CDKN2A), classify the evolutionary constraint across the variant's genomic window. | NM_000077.5(CDKN2A):c.381_393delinsGATGCG (p.Arg128fs) VARIANT_IN_GENE CDKN2A | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000077.5(CDKN2A):c.381_393delinsGATGCG (p.Arg128fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000077.5(CDKN2A):c.381_393delinsGATGCG (p.Arg128fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated"... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000077.5(CDKN2A):c.381_393delinsGATGCG (p.Arg128fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr9",
"pos": 21970966,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.24... | [
{
"source_db": "ClinVar",
"source_id": "CDKN2A",
"text": "NM_000077.5(CDKN2A):c.381_393delinsGATGCG (p.Arg128fs) VARIANT_IN_GENE CDKN2A",
"confidence": 1
}
] | {
"variant": "NM_000077.5(CDKN2A):c.381_393delinsGATGCG (p.Arg128fs)",
"gene": "CDKN2A",
"mean_phylop": 0.666,
"track": "phyloP100way"
} | 1 |
co_cons_00235 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000002.11:g.(?_47596286)_(47630542_47635539)del (in gene EPCAM), classify the evolutionary constraint across the variant's genomic window. | NC_000002.11:g.(?_47596286)_(47630542_47635539)del VARIANT_IN_GENE EPCAM | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000002.11:g.(?_47596286)_(47630542_47635539)del",
"source_node_type": "VARIANT",
"source_node_label": "NC_000002.11:g.(?_47596286)_(47630542_47635539)del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NC_000002.11:g.(?_47596286)_(47630542_47635539)del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr2",
"pos": 47596286,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.293180... | [
{
"source_db": "ClinVar",
"source_id": "EPCAM",
"text": "NC_000002.11:g.(?_47596286)_(47630542_47635539)del VARIANT_IN_GENE EPCAM",
"confidence": 1
}
] | {
"variant": "NC_000002.11:g.(?_47596286)_(47630542_47635539)del",
"gene": "EPCAM",
"mean_phylop": -0.079,
"track": "phyloP100way"
} | 1 |
co_cons_00236 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 5q35.2-35.3(chr5:175989092-178009412)x1 (in gene ARL10), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 5q35.2-35.3(chr5:175989092-178009412)x1 VARIANT_IN_GENE ARL10 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 5q35.2-35.3(chr5:175989092-178009412)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 5q35.2-35.3(chr5:175989092-178009412)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | C | [
"A. not conserved (mean phyloP < 0.0)",
"B. highly conserved (mean phyloP > 1.5)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 5q35.2-35.3(chr5:175989092-178009412)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr5",
"pos": 175989092,
"track": "phyloP100way",
"window": 20,
"scores": [
0.17719... | [
{
"source_db": "ClinVar",
"source_id": "ARL10",
"text": "GRCh38/hg38 5q35.2-35.3(chr5:175989092-178009412)x1 VARIANT_IN_GENE ARL10",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 5q35.2-35.3(chr5:175989092-178009412)x1",
"gene": "ARL10",
"mean_phylop": 0.212,
"track": "phyloP100way"
} | 1 |
co_cons_00237 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh38/hg38 17q21.31(chr17:45516110-46211895)x1 (in gene CRHR1), classify the evolutionary constraint across the variant's genomic window. | GRCh38/hg38 17q21.31(chr17:45516110-46211895)x1 VARIANT_IN_GENE CRHR1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh38/hg38 17q21.31(chr17:45516110-46211895)x1",
"source_node_type": "VARIANT",
"source_node_label": "GRCh38/hg38 17q21.31(chr17:45516110-46211895)x1",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh38/hg38 17q21.31(chr17:45516110-46211895)x1",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr17",
"pos": 45516110,
"track": "phyloP100way",
"window": 20,
"scores": [
-0.00767717... | [
{
"source_db": "ClinVar",
"source_id": "CRHR1",
"text": "GRCh38/hg38 17q21.31(chr17:45516110-46211895)x1 VARIANT_IN_GENE CRHR1",
"confidence": 1
}
] | {
"variant": "GRCh38/hg38 17q21.31(chr17:45516110-46211895)x1",
"gene": "CRHR1",
"mean_phylop": 0.153,
"track": "phyloP100way"
} | 1 |
co_cons_00238 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 20q11.21-11.23(chr20:29833608-35087952)x3 (in gene AAR2), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 20q11.21-11.23(chr20:29833608-35087952)x3 VARIANT_IN_GENE AAR2 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 20q11.21-11.23(chr20:29833608-35087952)x3",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 20q11.21-11.23(chr20:29833608-35087952)x3",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | A | [
"A. weakly conserved (mean phyloP 0.0-1.5)",
"B. highly conserved (mean phyloP > 1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 20q11.21-11.23(chr20:29833608-35087952)x3",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr20",
"pos": 29833608,
"track": "phyloP100way",
"window": 20,
"scores": [
0.150... | [
{
"source_db": "ClinVar",
"source_id": "AAR2",
"text": "GRCh37/hg19 20q11.21-11.23(chr20:29833608-35087952)x3 VARIANT_IN_GENE AAR2",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 20q11.21-11.23(chr20:29833608-35087952)x3",
"gene": "AAR2",
"mean_phylop": 0.069,
"track": "phyloP100way"
} | 1 |
co_cons_00239 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_002303.6(LEPR):c.1226C>A (p.Ala409Glu) (in gene LEPR), classify the evolutionary constraint across the variant's genomic window. | NM_002303.6(LEPR):c.1226C>A (p.Ala409Glu) VARIANT_IN_GENE LEPR | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_002303.6(LEPR):c.1226C>A (p.Ala409Glu)",
"source_node_type": "VARIANT",
"source_node_label": "NM_002303.6(LEPR):c.1226C>A (p.Ala409Glu)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_002303.6(LEPR):c.1226C>A (p.Ala409Glu)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr1",
"pos": 65601623,
"track": "phyloP100way",
"window": 20,
"scores": [
0.0759764,
... | [
{
"source_db": "ClinVar",
"source_id": "LEPR",
"text": "NM_002303.6(LEPR):c.1226C>A (p.Ala409Glu) VARIANT_IN_GENE LEPR",
"confidence": 1
}
] | {
"variant": "NM_002303.6(LEPR):c.1226C>A (p.Ala409Glu)",
"gene": "LEPR",
"mean_phylop": 2.049,
"track": "phyloP100way"
} | 1 |
co_cons_00240 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000011.9:g.(?_64522783)_(66283694_?)del (in gene AP5B1), classify the evolutionary constraint across the variant's genomic window. | NC_000011.9:g.(?_64522783)_(66283694_?)del VARIANT_IN_GENE AP5B1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000011.9:g.(?_64522783)_(66283694_?)del",
"source_node_type": "VARIANT",
"source_node_label": "NC_000011.9:g.(?_64522783)_(66283694_?)del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NC_000011.9:g.(?_64522783)_(66283694_?)del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr11",
"pos": 64522783,
"track": "phyloP100way",
"window": 20,
"scores": [
0.561929,
... | [
{
"source_db": "ClinVar",
"source_id": "AP5B1",
"text": "NC_000011.9:g.(?_64522783)_(66283694_?)del VARIANT_IN_GENE AP5B1",
"confidence": 1
}
] | {
"variant": "NC_000011.9:g.(?_64522783)_(66283694_?)del",
"gene": "AP5B1",
"mean_phylop": 0.151,
"track": "phyloP100way"
} | 1 |
co_cons_00241 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_012120.3(CD2AP):c.865_868del (p.Thr289fs) (in gene CD2AP), classify the evolutionary constraint across the variant's genomic window. | NM_012120.3(CD2AP):c.865_868del (p.Thr289fs) VARIANT_IN_GENE CD2AP | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_012120.3(CD2AP):c.865_868del (p.Thr289fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_012120.3(CD2AP):c.865_868del (p.Thr289fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | A | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_012120.3(CD2AP):c.865_868del (p.Thr289fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr6",
"pos": 47577061,
"track": "phyloP100way",
"window": 20,
"scores": [
4.77078,
... | [
{
"source_db": "ClinVar",
"source_id": "CD2AP",
"text": "NM_012120.3(CD2AP):c.865_868del (p.Thr289fs) VARIANT_IN_GENE CD2AP",
"confidence": 1
}
] | {
"variant": "NM_012120.3(CD2AP):c.865_868del (p.Thr289fs)",
"gene": "CD2AP",
"mean_phylop": 3.936,
"track": "phyloP100way"
} | 1 |
co_cons_00242 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for GRCh37/hg19 9q34.3(chr9:138225001-141015001) (in gene KCNT1), classify the evolutionary constraint across the variant's genomic window. | GRCh37/hg19 9q34.3(chr9:138225001-141015001) VARIANT_IN_GENE KCNT1 | {
"steps": [
{
"hop": 1,
"source_node_id": "GRCh37/hg19 9q34.3(chr9:138225001-141015001)",
"source_node_type": "VARIANT",
"source_node_label": "GRCh37/hg19 9q34.3(chr9:138225001-141015001)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "GRCh37/hg19 9q34.3(chr9:138225001-141015001)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr9",
"pos": 138225001,
"track": "phyloP100way",
"window": 20,
"scores": [
-1.01872,
... | [
{
"source_db": "ClinVar",
"source_id": "KCNT1",
"text": "GRCh37/hg19 9q34.3(chr9:138225001-141015001) VARIANT_IN_GENE KCNT1",
"confidence": 1
}
] | {
"variant": "GRCh37/hg19 9q34.3(chr9:138225001-141015001)",
"gene": "KCNT1",
"mean_phylop": -0.489,
"track": "phyloP100way"
} | 1 |
co_cons_00243 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_000044.6(AR):c.260dup (p.Gln88fs) (in gene AR), classify the evolutionary constraint across the variant's genomic window. | NM_000044.6(AR):c.260dup (p.Gln88fs) VARIANT_IN_GENE AR | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000044.6(AR):c.260dup (p.Gln88fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000044.6(AR):c.260dup (p.Gln88fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. highly conserved (mean phyloP > 1.5)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. not conserved (mean phyloP < 0.0)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_000044.6(AR):c.260dup (p.Gln88fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chrX",
"pos": 67545405,
"track": "phyloP100way",
"window": 20,
"scores": [
0.363984,
1.368... | [
{
"source_db": "ClinVar",
"source_id": "AR",
"text": "NM_000044.6(AR):c.260dup (p.Gln88fs) VARIANT_IN_GENE AR",
"confidence": 1
}
] | {
"variant": "NM_000044.6(AR):c.260dup (p.Gln88fs)",
"gene": "AR",
"mean_phylop": 0.7000000000000001,
"track": "phyloP100way"
} | 1 |
co_cons_00244 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NM_001127511.3(APC):c.-192A>G (in gene LOC129994371), classify the evolutionary constraint across the variant's genomic window. | NM_001127511.3(APC):c.-192A>G VARIANT_IN_GENE LOC129994371 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001127511.3(APC):c.-192A>G",
"source_node_type": "VARIANT",
"source_node_label": "NM_001127511.3(APC):c.-192A>G",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
"edge_source_d... | C | [
"A. highly conserved (mean phyloP > 1.5)",
"B. not conserved (mean phyloP < 0.0)",
"C. weakly conserved (mean phyloP 0.0-1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_001127511.3(APC):c.-192A>G",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr5",
"pos": 112707526,
"track": "phyloP100way",
"window": 20,
"scores": [
-5.09469,
1.56982,
... | [
{
"source_db": "ClinVar",
"source_id": "LOC129994371",
"text": "NM_001127511.3(APC):c.-192A>G VARIANT_IN_GENE LOC129994371",
"confidence": 1
}
] | {
"variant": "NM_001127511.3(APC):c.-192A>G",
"gene": "LOC129994371",
"mean_phylop": 1.334,
"track": "phyloP100way"
} | 1 |
co_cons_00245 | conservation_reasoning | coding_variant | easy | 1 | Using the phyloP conservation track provided for NC_000014.8:g.(?_20915399)_(22005055_?)del (in gene OR6S1), classify the evolutionary constraint across the variant's genomic window. | NC_000014.8:g.(?_20915399)_(22005055_?)del VARIANT_IN_GENE OR6S1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NC_000014.8:g.(?_20915399)_(22005055_?)del",
"source_node_type": "VARIANT",
"source_node_label": "NC_000014.8:g.(?_20915399)_(22005055_?)del",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | B | [
"A. not conserved (mean phyloP < 0.0)",
"B. weakly conserved (mean phyloP 0.0-1.5)",
"C. highly conserved (mean phyloP > 1.5)"
] | [
"conservation"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NC_000014.8:g.(?_20915399)_(22005055_?)del",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr14",
"pos": 20915399,
"track": "phyloP100way",
"window": 20,
"scores": [
0.0558189,
... | [
{
"source_db": "ClinVar",
"source_id": "OR6S1",
"text": "NC_000014.8:g.(?_20915399)_(22005055_?)del VARIANT_IN_GENE OR6S1",
"confidence": 1
}
] | {
"variant": "NC_000014.8:g.(?_20915399)_(22005055_?)del",
"gene": "OR6S1",
"mean_phylop": 0.059000000000000004,
"track": "phyloP100way"
} | 1 |
co_stru_00000 | structural_effect | coding_variant | easy | 1 | NM_000760.4(CSF3R):c.1633del (p.Leu545fs) introduces a premature truncation at residue 545 of CSF3R's 836-residue protein product (AlphaFold model, mean pLDDT 73.68). Approximately how much of the protein is lost downstream of the truncation? | NM_000760.4(CSF3R):c.1633del (p.Leu545fs) VARIANT_IN_GENE CSF3R | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000760.4(CSF3R):c.1633del (p.Leu545fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000760.4(CSF3R):c.1633del (p.Leu545fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | C | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CSF3R",
"source_db": "UniProt",
"payload": {
"accession": "Q99062",
"sequence": "MARLGNCSLTWAALIILLLPGSLEECGHISVSAPIVHLGDPITASCIIKQNCSHLDPEPQILWRLGAELQPGGRQQRLSDGTQESIITLPHLNHTQAFLSCCLNWGNSLQILDQVELRAGYPPAIPHNLSCLM... | [
{
"source_db": "ClinVar",
"source_id": "CSF3R",
"text": "NM_000760.4(CSF3R):c.1633del (p.Leu545fs) VARIANT_IN_GENE CSF3R",
"confidence": 1
}
] | {
"variant": "NM_000760.4(CSF3R):c.1633del (p.Leu545fs)",
"gene": "CSF3R",
"truncation_residue": 545,
"protein_length": 836,
"fraction_lost": 0.34800000000000003
} | 1 |
co_stru_00001 | structural_effect | coding_variant | easy | 1 | NM_000314.8(PTEN):c.638del (p.Pro213fs) introduces a premature truncation at residue 213 of PTEN's 403-residue protein product (AlphaFold model, mean pLDDT 83.03). Approximately how much of the protein is lost downstream of the truncation? | NM_000314.8(PTEN):c.638del (p.Pro213fs) VARIANT_IN_GENE PTEN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000314.8(PTEN):c.638del (p.Pro213fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000314.8(PTEN):c.638del (p.Pro213fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | A | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"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": "PTEN",
"text": "NM_000314.8(PTEN):c.638del (p.Pro213fs) VARIANT_IN_GENE PTEN",
"confidence": 1
}
] | {
"variant": "NM_000314.8(PTEN):c.638del (p.Pro213fs)",
"gene": "PTEN",
"truncation_residue": 213,
"protein_length": 403,
"fraction_lost": 0.47100000000000003
} | 1 |
co_stru_00002 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.50_53dup (p.Ser19fs) introduces a premature truncation at residue 19 of CHEK2's 543-residue protein product (AlphaFold model, mean pLDDT 76.18). Approximately how much of the protein is lost downstream of the truncation? | NM_007194.4(CHEK2):c.50_53dup (p.Ser19fs) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.50_53dup (p.Ser19fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.50_53dup (p.Ser19fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | C | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"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": "CHEK2",
"text": "NM_007194.4(CHEK2):c.50_53dup (p.Ser19fs) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.50_53dup (p.Ser19fs)",
"gene": "CHEK2",
"truncation_residue": 19,
"protein_length": 543,
"fraction_lost": 0.965
} | 1 |
co_stru_00003 | structural_effect | coding_variant | easy | 1 | NM_001008212.2(OPTN):c.1103del (p.Met368fs) introduces a premature truncation at residue 368 of OPTN's 577-residue protein product (AlphaFold model, mean pLDDT 77.26). Approximately how much of the protein is lost downstream of the truncation? | NM_001008212.2(OPTN):c.1103del (p.Met368fs) VARIANT_IN_GENE OPTN | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001008212.2(OPTN):c.1103del (p.Met368fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001008212.2(OPTN):c.1103del (p.Met368fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | C | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "OPTN",
"source_db": "UniProt",
"payload": {
"accession": "Q96CV9",
"sequence": "MSHQPLSCLTEKEDSPSESTGNGPPHLAHPNLDTFTPEELLQQMKELLTENHQLKEAMKLNNQAMKGRFEELSAWTEKQKEERQFFEIQSKEAKERLMALSHENEKLKEELGKLKGKSERSSEDPTDDSRLPRA... | [
{
"source_db": "ClinVar",
"source_id": "OPTN",
"text": "NM_001008212.2(OPTN):c.1103del (p.Met368fs) VARIANT_IN_GENE OPTN",
"confidence": 1
}
] | {
"variant": "NM_001008212.2(OPTN):c.1103del (p.Met368fs)",
"gene": "OPTN",
"truncation_residue": 368,
"protein_length": 577,
"fraction_lost": 0.362
} | 1 |
co_stru_00004 | structural_effect | coding_variant | easy | 1 | NM_000546.6(TP53):c.324_331delinsAAA (p.Phe109fs) introduces a premature truncation at residue 109 of TP53's 393-residue protein product (AlphaFold model, mean pLDDT 75.05). Approximately how much of the protein is lost downstream of the truncation? | NM_000546.6(TP53):c.324_331delinsAAA (p.Phe109fs) VARIANT_IN_GENE TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.324_331delinsAAA (p.Phe109fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.324_331delinsAAA (p.Phe109fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"e... | A | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "TP53",
"text": "NM_000546.6(TP53):c.324_331delinsAAA (p.Phe109fs) VARIANT_IN_GENE TP53",
"confidence": 1
}
] | {
"variant": "NM_000546.6(TP53):c.324_331delinsAAA (p.Phe109fs)",
"gene": "TP53",
"truncation_residue": 109,
"protein_length": 393,
"fraction_lost": 0.723
} | 1 |
co_stru_00005 | structural_effect | coding_variant | easy | 1 | NM_001903.5(CTNNA1):c.1870dup (p.Asp624fs) introduces a premature truncation at residue 624 of CTNNA1's 906-residue protein product (AlphaFold model, mean pLDDT 82.94). Approximately how much of the protein is lost downstream of the truncation? | NM_001903.5(CTNNA1):c.1870dup (p.Asp624fs) VARIANT_IN_GENE CTNNA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001903.5(CTNNA1):c.1870dup (p.Asp624fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001903.5(CTNNA1):c.1870dup (p.Asp624fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | B | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CTNNA1",
"source_db": "UniProt",
"payload": {
"accession": "P35221",
"sequence": "MTAVHAGNINFKWDPKSLEIRTLAVERLLEPLVTQVTTLVNTNSKGPSNKKRGRSKKAHVLAASVEQATENFLEKGDKIAKESQFLKEELVAAVEDVRKQGDLMKAAAGEFADDPCSSVKRGNMVRAARALL... | [
{
"source_db": "ClinVar",
"source_id": "CTNNA1",
"text": "NM_001903.5(CTNNA1):c.1870dup (p.Asp624fs) VARIANT_IN_GENE CTNNA1",
"confidence": 1
}
] | {
"variant": "NM_001903.5(CTNNA1):c.1870dup (p.Asp624fs)",
"gene": "CTNNA1",
"truncation_residue": 624,
"protein_length": 906,
"fraction_lost": 0.311
} | 1 |
co_stru_00006 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.1760_1761del (p.Ile587fs) introduces a premature truncation at residue 587 of BRCA1's 1863-residue protein product (AlphaFold model, mean pLDDT 41.59). Approximately how much of the protein is lost downstream of the truncation? | NM_007294.4(BRCA1):c.1760_1761del (p.Ile587fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.1760_1761del (p.Ile587fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.1760_1761del (p.Ile587fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_co... | C | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"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": "BRCA1",
"text": "NM_007294.4(BRCA1):c.1760_1761del (p.Ile587fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.1760_1761del (p.Ile587fs)",
"gene": "BRCA1",
"truncation_residue": 587,
"protein_length": 1863,
"fraction_lost": 0.685
} | 1 |
co_stru_00007 | structural_effect | coding_variant | easy | 1 | NM_000179.3(MSH6):c.3080dup (p.Ser1028fs) introduces a premature truncation at residue 1028 of MSH6's 1360-residue protein product (AlphaFold model, mean pLDDT 77.09). Approximately how much of the protein is lost downstream of the truncation? | NM_000179.3(MSH6):c.3080dup (p.Ser1028fs) VARIANT_IN_GENE MSH6 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000179.3(MSH6):c.3080dup (p.Ser1028fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000179.3(MSH6):c.3080dup (p.Ser1028fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence":... | C | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "MSH6",
"text": "NM_000179.3(MSH6):c.3080dup (p.Ser1028fs) VARIANT_IN_GENE MSH6",
"confidence": 1
}
] | {
"variant": "NM_000179.3(MSH6):c.3080dup (p.Ser1028fs)",
"gene": "MSH6",
"truncation_residue": 1028,
"protein_length": 1360,
"fraction_lost": 0.244
} | 1 |
co_stru_00008 | structural_effect | coding_variant | easy | 1 | NM_000249.4(MLH1):c.2031_2041del (p.Lys678fs) introduces a premature truncation at residue 678 of MLH1's 756-residue protein product (AlphaFold model, mean pLDDT 77.31). Approximately how much of the protein is lost downstream of the truncation? | NM_000249.4(MLH1):c.2031_2041del (p.Lys678fs) VARIANT_IN_GENE MLH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000249.4(MLH1):c.2031_2041del (p.Lys678fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000249.4(MLH1):c.2031_2041del (p.Lys678fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | C | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "ClinVar",
"source_id": "MLH1",
"text": "NM_000249.4(MLH1):c.2031_2041del (p.Lys678fs) VARIANT_IN_GENE MLH1",
"confidence": 1
}
] | {
"variant": "NM_000249.4(MLH1):c.2031_2041del (p.Lys678fs)",
"gene": "MLH1",
"truncation_residue": 678,
"protein_length": 756,
"fraction_lost": 0.10300000000000001
} | 1 |
co_stru_00009 | structural_effect | coding_variant | easy | 1 | NM_058216.3(RAD51C):c.1000del (p.Glu334fs) introduces a premature truncation at residue 334 of RAD51C's 376-residue protein product (AlphaFold model, mean pLDDT 84.36). Approximately how much of the protein is lost downstream of the truncation? | NM_058216.3(RAD51C):c.1000del (p.Glu334fs) VARIANT_IN_GENE RAD51C | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_058216.3(RAD51C):c.1000del (p.Glu334fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_058216.3(RAD51C):c.1000del (p.Glu334fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | A | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"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": "RAD51C",
"text": "NM_058216.3(RAD51C):c.1000del (p.Glu334fs) VARIANT_IN_GENE RAD51C",
"confidence": 1
}
] | {
"variant": "NM_058216.3(RAD51C):c.1000del (p.Glu334fs)",
"gene": "RAD51C",
"truncation_residue": 334,
"protein_length": 376,
"fraction_lost": 0.112
} | 1 |
co_stru_00010 | structural_effect | coding_variant | easy | 1 | NM_020919.4(ALS2):c.2016_2026del (p.Val673fs) introduces a premature truncation at residue 673 of ALS2's 1657-residue protein product (AlphaFold model, mean pLDDT 74.05). Approximately how much of the protein is lost downstream of the truncation? | NM_020919.4(ALS2):c.2016_2026del (p.Val673fs) VARIANT_IN_GENE ALS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_020919.4(ALS2):c.2016_2026del (p.Val673fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_020919.4(ALS2):c.2016_2026del (p.Val673fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"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": "ALS2",
"text": "NM_020919.4(ALS2):c.2016_2026del (p.Val673fs) VARIANT_IN_GENE ALS2",
"confidence": 1
}
] | {
"variant": "NM_020919.4(ALS2):c.2016_2026del (p.Val673fs)",
"gene": "ALS2",
"truncation_residue": 673,
"protein_length": 1657,
"fraction_lost": 0.594
} | 1 |
co_stru_00011 | structural_effect | coding_variant | easy | 1 | NM_024675.4(PALB2):c.2104_2107delinsTAA (p.Ile702_Leu703delinsTer) introduces a premature truncation at residue 702 of PALB2's 1186-residue protein product (AlphaFold model, mean pLDDT 53.81). Approximately how much of the protein is lost downstream of the truncation? | NM_024675.4(PALB2):c.2104_2107delinsTAA (p.Ile702_Leu703delinsTer) VARIANT_IN_GENE PALB2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_024675.4(PALB2):c.2104_2107delinsTAA (p.Ile702_Leu703delinsTer)",
"source_node_type": "VARIANT",
"source_node_label": "NM_024675.4(PALB2):c.2104_2107delinsTAA (p.Ile702_Leu703delinsTer)",
"edge_relation": "VARIANT_IN_GENE",
"edge_e... | C | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"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": "PALB2",
"text": "NM_024675.4(PALB2):c.2104_2107delinsTAA (p.Ile702_Leu703delinsTer) VARIANT_IN_GENE PALB2",
"confidence": 1
}
] | {
"variant": "NM_024675.4(PALB2):c.2104_2107delinsTAA (p.Ile702_Leu703delinsTer)",
"gene": "PALB2",
"truncation_residue": 702,
"protein_length": 1186,
"fraction_lost": 0.40800000000000003
} | 1 |
co_stru_00012 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.3415dup (p.Ser1139fs) introduces a premature truncation at residue 1139 of BRCA1's 1863-residue protein product (AlphaFold model, mean pLDDT 41.59). Approximately how much of the protein is lost downstream of the truncation? | NM_007294.4(BRCA1):c.3415dup (p.Ser1139fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.3415dup (p.Ser1139fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.3415dup (p.Ser1139fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence... | B | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "BRCA1",
"text": "NM_007294.4(BRCA1):c.3415dup (p.Ser1139fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.3415dup (p.Ser1139fs)",
"gene": "BRCA1",
"truncation_residue": 1139,
"protein_length": 1863,
"fraction_lost": 0.389
} | 1 |
co_stru_00013 | structural_effect | coding_variant | easy | 1 | NM_000546.6(TP53):c.846del (p.Arg283fs) introduces a premature truncation at residue 283 of TP53's 393-residue protein product (AlphaFold model, mean pLDDT 75.05). Approximately how much of the protein is lost downstream of the truncation? | NM_000546.6(TP53):c.846del (p.Arg283fs) VARIANT_IN_GENE TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.846del (p.Arg283fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.846del (p.Arg283fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"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": "TP53",
"text": "NM_000546.6(TP53):c.846del (p.Arg283fs) VARIANT_IN_GENE TP53",
"confidence": 1
}
] | {
"variant": "NM_000546.6(TP53):c.846del (p.Arg283fs)",
"gene": "TP53",
"truncation_residue": 283,
"protein_length": 393,
"fraction_lost": 0.28
} | 1 |
co_stru_00014 | structural_effect | coding_variant | easy | 1 | NM_004380.3(CREBBP):c.3099_3102del (p.Glu1034fs) introduces a premature truncation at residue 1034 of CREBBP's 2442-residue protein product (AlphaFold model, mean pLDDT 52.52). Approximately how much of the protein is lost downstream of the truncation? | NM_004380.3(CREBBP):c.3099_3102del (p.Glu1034fs) VARIANT_IN_GENE CREBBP | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004380.3(CREBBP):c.3099_3102del (p.Glu1034fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004380.3(CREBBP):c.3099_3102del (p.Glu1034fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | A | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"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": "CREBBP",
"text": "NM_004380.3(CREBBP):c.3099_3102del (p.Glu1034fs) VARIANT_IN_GENE CREBBP",
"confidence": 1
}
] | {
"variant": "NM_004380.3(CREBBP):c.3099_3102del (p.Glu1034fs)",
"gene": "CREBBP",
"truncation_residue": 1034,
"protein_length": 2442,
"fraction_lost": 0.577
} | 1 |
co_stru_00015 | structural_effect | coding_variant | easy | 1 | NM_004360.5(CDH1):c.1340_1346del (p.Lys447fs) introduces a premature truncation at residue 447 of CDH1's 882-residue protein product (AlphaFold model, mean pLDDT 79.16). Approximately how much of the protein is lost downstream of the truncation? | NM_004360.5(CDH1):c.1340_1346del (p.Lys447fs) VARIANT_IN_GENE CDH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_004360.5(CDH1):c.1340_1346del (p.Lys447fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_004360.5(CDH1):c.1340_1346del (p.Lys447fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | C | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"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": "CDH1",
"text": "NM_004360.5(CDH1):c.1340_1346del (p.Lys447fs) VARIANT_IN_GENE CDH1",
"confidence": 1
}
] | {
"variant": "NM_004360.5(CDH1):c.1340_1346del (p.Lys447fs)",
"gene": "CDH1",
"truncation_residue": 447,
"protein_length": 882,
"fraction_lost": 0.493
} | 1 |
co_stru_00016 | structural_effect | coding_variant | easy | 1 | NM_024675.4(PALB2):c.50T>A (p.Leu17Ter) introduces a premature truncation at residue 17 of PALB2's 1186-residue protein product (AlphaFold model, mean pLDDT 53.81). Approximately how much of the protein is lost downstream of the truncation? | NM_024675.4(PALB2):c.50T>A (p.Leu17Ter) VARIANT_IN_GENE PALB2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_024675.4(PALB2):c.50T>A (p.Leu17Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_024675.4(PALB2):c.50T>A (p.Leu17Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"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": "PALB2",
"text": "NM_024675.4(PALB2):c.50T>A (p.Leu17Ter) VARIANT_IN_GENE PALB2",
"confidence": 1
}
] | {
"variant": "NM_024675.4(PALB2):c.50T>A (p.Leu17Ter)",
"gene": "PALB2",
"truncation_residue": 17,
"protein_length": 1186,
"fraction_lost": 0.986
} | 1 |
co_stru_00017 | structural_effect | coding_variant | easy | 1 | NM_000465.4(BARD1):c.2300_2301dup (p.Met768Ter) introduces a premature truncation at residue 768 of BARD1's 777-residue protein product (AlphaFold model, mean pLDDT 64.16). Approximately how much of the protein is lost downstream of the truncation? | NM_000465.4(BARD1):c.2300_2301dup (p.Met768Ter) VARIANT_IN_GENE BARD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000465.4(BARD1):c.2300_2301dup (p.Met768Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000465.4(BARD1):c.2300_2301dup (p.Met768Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_... | A | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"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": "BARD1",
"text": "NM_000465.4(BARD1):c.2300_2301dup (p.Met768Ter) VARIANT_IN_GENE BARD1",
"confidence": 1
}
] | {
"variant": "NM_000465.4(BARD1):c.2300_2301dup (p.Met768Ter)",
"gene": "BARD1",
"truncation_residue": 768,
"protein_length": 777,
"fraction_lost": 0.012
} | 1 |
co_stru_00018 | structural_effect | coding_variant | easy | 1 | NM_007194.4(CHEK2):c.980delinsTG (p.Tyr327fs) introduces a premature truncation at residue 327 of CHEK2's 543-residue protein product (AlphaFold model, mean pLDDT 76.18). Approximately how much of the protein is lost downstream of the truncation? | NM_007194.4(CHEK2):c.980delinsTG (p.Tyr327fs) VARIANT_IN_GENE CHEK2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007194.4(CHEK2):c.980delinsTG (p.Tyr327fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007194.4(CHEK2):c.980delinsTG (p.Tyr327fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_conf... | A | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"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": "CHEK2",
"text": "NM_007194.4(CHEK2):c.980delinsTG (p.Tyr327fs) VARIANT_IN_GENE CHEK2",
"confidence": 1
}
] | {
"variant": "NM_007194.4(CHEK2):c.980delinsTG (p.Tyr327fs)",
"gene": "CHEK2",
"truncation_residue": 327,
"protein_length": 543,
"fraction_lost": 0.398
} | 1 |
co_stru_00019 | structural_effect | coding_variant | easy | 1 | NM_000546.6(TP53):c.631_632del (p.Thr211fs) introduces a premature truncation at residue 211 of TP53's 393-residue protein product (AlphaFold model, mean pLDDT 75.05). Approximately how much of the protein is lost downstream of the truncation? | NM_000546.6(TP53):c.631_632del (p.Thr211fs) VARIANT_IN_GENE TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.631_632del (p.Thr211fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.631_632del (p.Thr211fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | B | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"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": "TP53",
"text": "NM_000546.6(TP53):c.631_632del (p.Thr211fs) VARIANT_IN_GENE TP53",
"confidence": 1
}
] | {
"variant": "NM_000546.6(TP53):c.631_632del (p.Thr211fs)",
"gene": "TP53",
"truncation_residue": 211,
"protein_length": 393,
"fraction_lost": 0.463
} | 1 |
co_stru_00020 | structural_effect | coding_variant | easy | 1 | NM_000044.6(AR):c.1341T>A (p.Tyr447Ter) introduces a premature truncation at residue 447 of AR's 920-residue protein product (AlphaFold model, mean pLDDT 57.25). Approximately how much of the protein is lost downstream of the truncation? | NM_000044.6(AR):c.1341T>A (p.Tyr447Ter) VARIANT_IN_GENE AR | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000044.6(AR):c.1341T>A (p.Tyr447Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000044.6(AR):c.1341T>A (p.Tyr447Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "AR",
"source_db": "UniProt",
"payload": {
"accession": "P10275",
"sequence": "MEVQLGLGRVYPRPPSKTYRGAFQNLFQSVREVIQNPGPRHPEAASAAPPGASLLLLQQQQQQQQQQQQQQQQQQQQQQQETSPRQQQQQQGEDGSPQAHRRGPTGYLVLDEEQQPSQPQSALECHPERGCVPEPG... | [
{
"source_db": "ClinVar",
"source_id": "AR",
"text": "NM_000044.6(AR):c.1341T>A (p.Tyr447Ter) VARIANT_IN_GENE AR",
"confidence": 1
}
] | {
"variant": "NM_000044.6(AR):c.1341T>A (p.Tyr447Ter)",
"gene": "AR",
"truncation_residue": 447,
"protein_length": 920,
"fraction_lost": 0.514
} | 1 |
co_stru_00021 | structural_effect | coding_variant | easy | 1 | NM_022089.4(ATP13A2):c.1407_1428dup (p.Met477fs) introduces a premature truncation at residue 477 of ATP13A2's 1180-residue protein product (AlphaFold model, mean pLDDT 79.64). Approximately how much of the protein is lost downstream of the truncation? | NM_022089.4(ATP13A2):c.1407_1428dup (p.Met477fs) VARIANT_IN_GENE ATP13A2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_022089.4(ATP13A2):c.1407_1428dup (p.Met477fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_022089.4(ATP13A2):c.1407_1428dup (p.Met477fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edg... | A | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ATP13A2",
"source_db": "UniProt",
"payload": {
"accession": "Q9NQ11",
"sequence": "MSADSSPLVGSTPTGYGTLTIGTSIDPLSSSVSSVRLSGYCGSPWRVIGYHVVVWMMAGIPLLLFRWKPLWGVRLRLRPCNLAHAETLVIEIRDKEDSSWQLFTVQVQTEAIGEGSLEPSPQSQAEDGRSQ... | [
{
"source_db": "ClinVar",
"source_id": "ATP13A2",
"text": "NM_022089.4(ATP13A2):c.1407_1428dup (p.Met477fs) VARIANT_IN_GENE ATP13A2",
"confidence": 1
}
] | {
"variant": "NM_022089.4(ATP13A2):c.1407_1428dup (p.Met477fs)",
"gene": "ATP13A2",
"truncation_residue": 477,
"protein_length": 1180,
"fraction_lost": 0.596
} | 1 |
co_stru_00022 | structural_effect | coding_variant | easy | 1 | NM_001903.5(CTNNA1):c.1240A>T (p.Lys414Ter) introduces a premature truncation at residue 414 of CTNNA1's 906-residue protein product (AlphaFold model, mean pLDDT 82.94). Approximately how much of the protein is lost downstream of the truncation? | NM_001903.5(CTNNA1):c.1240A>T (p.Lys414Ter) VARIANT_IN_GENE CTNNA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001903.5(CTNNA1):c.1240A>T (p.Lys414Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001903.5(CTNNA1):c.1240A>T (p.Lys414Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | B | [
"A. a substantial portion (25-50%)",
"B. more than half the protein (>50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "CTNNA1",
"source_db": "UniProt",
"payload": {
"accession": "P35221",
"sequence": "MTAVHAGNINFKWDPKSLEIRTLAVERLLEPLVTQVTTLVNTNSKGPSNKKRGRSKKAHVLAASVEQATENFLEKGDKIAKESQFLKEELVAAVEDVRKQGDLMKAAAGEFADDPCSSVKRGNMVRAARALL... | [
{
"source_db": "ClinVar",
"source_id": "CTNNA1",
"text": "NM_001903.5(CTNNA1):c.1240A>T (p.Lys414Ter) VARIANT_IN_GENE CTNNA1",
"confidence": 1
}
] | {
"variant": "NM_001903.5(CTNNA1):c.1240A>T (p.Lys414Ter)",
"gene": "CTNNA1",
"truncation_residue": 414,
"protein_length": 906,
"fraction_lost": 0.543
} | 1 |
co_stru_00023 | structural_effect | coding_variant | easy | 1 | NM_000535.7(PMS2):c.481C>T (p.Gln161Ter) introduces a premature truncation at residue 161 of PMS2's 862-residue protein product (AlphaFold model, mean pLDDT 70.97). Approximately how much of the protein is lost downstream of the truncation? | NM_000535.7(PMS2):c.481C>T (p.Gln161Ter) VARIANT_IN_GENE PMS2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000535.7(PMS2):c.481C>T (p.Gln161Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000535.7(PMS2):c.481C>T (p.Gln161Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | A | [
"A. more than half the protein (>50%)",
"B. a small C-terminal portion (<25%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "PMS2",
"source_db": "UniProt",
"payload": {
"accession": "P54278",
"sequence": "MERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTR... | [
{
"source_db": "ClinVar",
"source_id": "PMS2",
"text": "NM_000535.7(PMS2):c.481C>T (p.Gln161Ter) VARIANT_IN_GENE PMS2",
"confidence": 1
}
] | {
"variant": "NM_000535.7(PMS2):c.481C>T (p.Gln161Ter)",
"gene": "PMS2",
"truncation_residue": 161,
"protein_length": 862,
"fraction_lost": 0.8130000000000001
} | 1 |
co_stru_00024 | structural_effect | coding_variant | easy | 1 | NM_007294.4(BRCA1):c.450del (p.Ser151fs) introduces a premature truncation at residue 151 of BRCA1's 1863-residue protein product (AlphaFold model, mean pLDDT 41.59). Approximately how much of the protein is lost downstream of the truncation? | NM_007294.4(BRCA1):c.450del (p.Ser151fs) VARIANT_IN_GENE BRCA1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_007294.4(BRCA1):c.450del (p.Ser151fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_007294.4(BRCA1):c.450del (p.Ser151fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | C | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"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": "BRCA1",
"text": "NM_007294.4(BRCA1):c.450del (p.Ser151fs) VARIANT_IN_GENE BRCA1",
"confidence": 1
}
] | {
"variant": "NM_007294.4(BRCA1):c.450del (p.Ser151fs)",
"gene": "BRCA1",
"truncation_residue": 151,
"protein_length": 1863,
"fraction_lost": 0.919
} | 1 |
co_stru_00025 | structural_effect | coding_variant | easy | 1 | NM_000057.4(BLM):c.1624del (p.Asp542fs) introduces a premature truncation at residue 542 of BLM's 1417-residue protein product (AlphaFold model, mean pLDDT 60.54). Approximately how much of the protein is lost downstream of the truncation? | NM_000057.4(BLM):c.1624del (p.Asp542fs) VARIANT_IN_GENE BLM | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000057.4(BLM):c.1624del (p.Asp542fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000057.4(BLM):c.1624del (p.Asp542fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "BLM",
"source_db": "UniProt",
"payload": {
"accession": "P54132",
"sequence": "MAAVPQNNLQEQLERHSARTLNNKLSLSKPKFSGFTFKKKTSSDNNVSVTNVSVAKTPVLRNKDVNVTEDFSFSEPLPNTTNQQRVKDFFKNAPAGQETQRGGSKSLLPDFLQTPKEVVCTTQNTPTVKKSRDTA... | [
{
"source_db": "ClinVar",
"source_id": "BLM",
"text": "NM_000057.4(BLM):c.1624del (p.Asp542fs) VARIANT_IN_GENE BLM",
"confidence": 1
}
] | {
"variant": "NM_000057.4(BLM):c.1624del (p.Asp542fs)",
"gene": "BLM",
"truncation_residue": 542,
"protein_length": 1417,
"fraction_lost": 0.618
} | 1 |
co_stru_00026 | structural_effect | coding_variant | easy | 1 | NM_000249.4(MLH1):c.825del (p.Ala275_Ile276insTer) introduces a premature truncation at residue 275 of MLH1's 756-residue protein product (AlphaFold model, mean pLDDT 77.31). Approximately how much of the protein is lost downstream of the truncation? | NM_000249.4(MLH1):c.825del (p.Ala275_Ile276insTer) VARIANT_IN_GENE MLH1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000249.4(MLH1):c.825del (p.Ala275_Ile276insTer)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000249.4(MLH1):c.825del (p.Ala275_Ile276insTer)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | C | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "MLH1",
"source_db": "UniProt",
"payload": {
"accession": "P40692",
"sequence": "MSFVAGVIRRLDETVVNRIAAGEVIQRPANAIKEMIENCLDAKSTSIQVIVKEGGLKLIQIQDNGTGIRKEDLDIVCERFTTSKLQSFEDLASISTYGFRGEALASISHVAHVTITTKTADGKCAYRASYSDGK... | [
{
"source_db": "ClinVar",
"source_id": "MLH1",
"text": "NM_000249.4(MLH1):c.825del (p.Ala275_Ile276insTer) VARIANT_IN_GENE MLH1",
"confidence": 1
}
] | {
"variant": "NM_000249.4(MLH1):c.825del (p.Ala275_Ile276insTer)",
"gene": "MLH1",
"truncation_residue": 275,
"protein_length": 756,
"fraction_lost": 0.636
} | 1 |
co_stru_00027 | structural_effect | coding_variant | easy | 1 | NM_000465.4(BARD1):c.786_799del (p.Ser263fs) introduces a premature truncation at residue 263 of BARD1's 777-residue protein product (AlphaFold model, mean pLDDT 64.16). Approximately how much of the protein is lost downstream of the truncation? | NM_000465.4(BARD1):c.786_799del (p.Ser263fs) VARIANT_IN_GENE BARD1 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000465.4(BARD1):c.786_799del (p.Ser263fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000465.4(BARD1):c.786_799del (p.Ser263fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confid... | C | [
"A. a substantial portion (25-50%)",
"B. a small C-terminal portion (<25%)",
"C. more than half the protein (>50%)"
] | [
"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": "BARD1",
"text": "NM_000465.4(BARD1):c.786_799del (p.Ser263fs) VARIANT_IN_GENE BARD1",
"confidence": 1
}
] | {
"variant": "NM_000465.4(BARD1):c.786_799del (p.Ser263fs)",
"gene": "BARD1",
"truncation_residue": 263,
"protein_length": 777,
"fraction_lost": 0.662
} | 1 |
co_stru_00028 | structural_effect | coding_variant | easy | 1 | NM_024675.4(PALB2):c.93dup (p.Leu32fs) introduces a premature truncation at residue 32 of PALB2's 1186-residue protein product (AlphaFold model, mean pLDDT 53.81). Approximately how much of the protein is lost downstream of the truncation? | NM_024675.4(PALB2):c.93dup (p.Leu32fs) VARIANT_IN_GENE PALB2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_024675.4(PALB2):c.93dup (p.Leu32fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_024675.4(PALB2):c.93dup (p.Leu32fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1,
... | C | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"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": "PALB2",
"text": "NM_024675.4(PALB2):c.93dup (p.Leu32fs) VARIANT_IN_GENE PALB2",
"confidence": 1
}
] | {
"variant": "NM_024675.4(PALB2):c.93dup (p.Leu32fs)",
"gene": "PALB2",
"truncation_residue": 32,
"protein_length": 1186,
"fraction_lost": 0.973
} | 1 |
co_stru_00029 | structural_effect | coding_variant | easy | 1 | NM_001098.3(ACO2):c.1832del (p.Asp611fs) introduces a premature truncation at residue 611 of ACO2's 780-residue protein product (AlphaFold model, mean pLDDT 95.43). Approximately how much of the protein is lost downstream of the truncation? | NM_001098.3(ACO2):c.1832del (p.Asp611fs) VARIANT_IN_GENE ACO2 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_001098.3(ACO2):c.1832del (p.Asp611fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_001098.3(ACO2):c.1832del (p.Asp611fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | C | [
"A. more than half the protein (>50%)",
"B. a substantial portion (25-50%)",
"C. a small C-terminal portion (<25%)"
] | [
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "sequence",
"tag": "protein_sequence",
"anchor_node_id": "ACO2",
"source_db": "UniProt",
"payload": {
"accession": "Q99798",
"sequence": "MAPYSLLVTRLQKALGVRQYHVASVLCQRAKVAMSHFEPNEYIHYDLLEKNINIVRKRLNRPLTLSEKIVYGHLDDPASQEIERGKSYLRLRPDRVAMQDATAQMAMLQFISSGLSKVAVPSTIHCDHLIEAQV... | [
{
"source_db": "ClinVar",
"source_id": "ACO2",
"text": "NM_001098.3(ACO2):c.1832del (p.Asp611fs) VARIANT_IN_GENE ACO2",
"confidence": 1
}
] | {
"variant": "NM_001098.3(ACO2):c.1832del (p.Asp611fs)",
"gene": "ACO2",
"truncation_residue": 611,
"protein_length": 780,
"fraction_lost": 0.217
} | 1 |
co_stru_00030 | structural_effect | coding_variant | easy | 1 | NM_005612.5(REST):c.831_832del (p.Cys278fs) introduces a premature truncation at residue 278 of REST's 1097-residue protein product (AlphaFold model, mean pLDDT 48.86). Approximately how much of the protein is lost downstream of the truncation? | NM_005612.5(REST):c.831_832del (p.Cys278fs) VARIANT_IN_GENE REST | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_005612.5(REST):c.831_832del (p.Cys278fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_005612.5(REST):c.831_832del (p.Cys278fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confiden... | C | [
"A. a small C-terminal portion (<25%)",
"B. a substantial portion (25-50%)",
"C. more than half the protein (>50%)"
] | [
"conservation",
"expression",
"protein_sequence",
"protein_structure"
] | [
{
"family": "evolutionary",
"tag": "conservation",
"anchor_node_id": "NM_005612.5(REST):c.831_832del (p.Cys278fs)",
"source_db": "UCSC_phyloP",
"payload": {
"chrom": "chr4",
"pos": 56911469,
"track": "phyloP100way",
"window": 20,
"scores": [
7.73886,
... | [
{
"source_db": "ClinVar",
"source_id": "REST",
"text": "NM_005612.5(REST):c.831_832del (p.Cys278fs) VARIANT_IN_GENE REST",
"confidence": 1
}
] | {
"variant": "NM_005612.5(REST):c.831_832del (p.Cys278fs)",
"gene": "REST",
"truncation_residue": 278,
"protein_length": 1097,
"fraction_lost": 0.747
} | 1 |
co_stru_00031 | structural_effect | coding_variant | easy | 1 | NM_000546.6(TP53):c.845_846insCACAAGAG (p.Arg283fs) introduces a premature truncation at residue 283 of TP53's 393-residue protein product (AlphaFold model, mean pLDDT 75.05). Approximately how much of the protein is lost downstream of the truncation? | NM_000546.6(TP53):c.845_846insCACAAGAG (p.Arg283fs) VARIANT_IN_GENE TP53 | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_000546.6(TP53):c.845_846insCACAAGAG (p.Arg283fs)",
"source_node_type": "VARIANT",
"source_node_label": "NM_000546.6(TP53):c.845_846insCACAAGAG (p.Arg283fs)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
... | C | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"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": "TP53",
"text": "NM_000546.6(TP53):c.845_846insCACAAGAG (p.Arg283fs) VARIANT_IN_GENE TP53",
"confidence": 1
}
] | {
"variant": "NM_000546.6(TP53):c.845_846insCACAAGAG (p.Arg283fs)",
"gene": "TP53",
"truncation_residue": 283,
"protein_length": 393,
"fraction_lost": 0.28
} | 1 |
co_stru_00032 | structural_effect | coding_variant | easy | 1 | NM_002303.6(LEPR):c.802C>T (p.Gln268Ter) introduces a premature truncation at residue 268 of LEPR's 1165-residue protein product (AlphaFold model, mean pLDDT 66.02). Approximately how much of the protein is lost downstream of the truncation? | NM_002303.6(LEPR):c.802C>T (p.Gln268Ter) VARIANT_IN_GENE LEPR | {
"steps": [
{
"hop": 1,
"source_node_id": "NM_002303.6(LEPR):c.802C>T (p.Gln268Ter)",
"source_node_type": "VARIANT",
"source_node_label": "NM_002303.6(LEPR):c.802C>T (p.Gln268Ter)",
"edge_relation": "VARIANT_IN_GENE",
"edge_evidence_type": "curated",
"edge_confidence": 1... | B | [
"A. a small C-terminal portion (<25%)",
"B. more than half the protein (>50%)",
"C. a substantial portion (25-50%)"
] | [
"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": "LEPR",
"text": "NM_002303.6(LEPR):c.802C>T (p.Gln268Ter) VARIANT_IN_GENE LEPR",
"confidence": 1
}
] | {
"variant": "NM_002303.6(LEPR):c.802C>T (p.Gln268Ter)",
"gene": "LEPR",
"truncation_residue": 268,
"protein_length": 1165,
"fraction_lost": 0.77
} | 1 |
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