{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA553770", "communityStandardTitle": [ "NM_015102.5(NPHP4):c.3175G>A (p.Ala1059Thr)" ], "externalRecords": { "COSMIC": [ { "@id": "http://cancer.sanger.ac.uk/cosmic/mutation/overview?id=1217708", "active": true, "id": "COSM1217708" } ], "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=493743[alleleid]", "alleleId": 493743, "preferredName": "NM_015102.5(NPHP4):c.3175G>A (p.Ala1059Thr)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/502319", "RCV": [ "RCV000765247", "RCV001098353", "RCV000592906", "RCV001098354", "RCV001054486" ], "variationId": 502319 } ], "ExAC": [ { "@id": "http://exac.broadinstitute.org/variant/1-5934587-C-T", "id": "1-5934587-C-T", "variant": "1:5934587 C / T" } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.5934587C>T?assembly=hg19", "id": "chr1:g.5934587C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr1:g.5874527C>T?assembly=hg38", "id": "chr1:g.5874527C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/202004152", "rs": 202004152 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-5934587-C-T?dataset=gnomad_r2_1", "id": "1-5934587-C-T", "variant": "1:5934587 C / T" } ], "gnomAD_3": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-5874527-C-T?dataset=gnomad_r3", "id": "1-5874527-C-T", "variant": "1:5874527 C / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/1-5874527-C-T?dataset=gnomad_r4", "id": "1-5874527-C-T", "variant": "1:5874527 C / T" } ] }, "genomicAlleles": [ { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 5874527, "referenceAllele": "C", "start": 5874526 } ], "hgvs": [ "NC_000001.11:g.5874527C>T", "CM000663.2:g.5874527C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000049" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 5934587, "referenceAllele": "C", "start": 5934586 } ], "hgvs": [ "NC_000001.10:g.5934587C>T", "CM000663.1:g.5934587C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000025" }, { "chromosome": "1", "coordinates": [ { "allele": "T", "end": 5857174, "referenceAllele": "C", "start": 5857173 } ], "hgvs": [ "NC_000001.9:g.5857174C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000001" }, { "coordinates": [ { "allele": "A", "end": 122945, "referenceAllele": "G", "start": 122944 } ], "hgvs": [ "NG_011724.2:g.122945G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS001929" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 3395, "referenceAllele": "G", "start": 3394 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "ENST00000378156.9:c.3175G>A" ], "proteinEffect": { "hgvs": "ENSP00000367398.4:p.Ala1059Thr", "hgvsWellDefined": "ENSP00000367398.4:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS752036", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000378156.9:c.3175G>A" }, "RefSeq": { "hgvs": "NM_015102.5:c.3175G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000367398.4:p.Ala1059Thr" }, "RefSeq": { "hgvs": "NP_055917.1:p.Ala1059Thr" } } } }, { "coordinates": [ { "allele": "A", "end": 3441, "referenceAllele": "G", "start": 3440 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "ENST00000378156.8:c.3175G>A" ], "proteinEffect": { "hgvs": "ENSP00000367398.4:p.Ala1059Thr", "hgvsWellDefined": "ENSP00000367398.4:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS271910" }, { "coordinates": [ { "allele": "A", "end": 3107, "referenceAllele": "G", "start": 3106 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "ENST00000378169.7:c.*2076G>A" ], "proteinEffect": { "hgvs": "ENSP00000367411.3:n.*2076G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS271918" }, { "coordinates": [ { "allele": "A", "end": 2907, "referenceAllele": "G", "start": 2906 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "ENST00000478423.6:n.2907G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS319035" }, { "coordinates": [ { "allele": "A", "end": 3990, "referenceAllele": "G", "start": 3989 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "ENST00000489180.6:c.*986G>A" ], "proteinEffect": { "hgvs": "ENSP00000423747.1:n.*986G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS327298" }, { "@id": "http://reg.genome.network/allele/PA2826800569", "coordinates": [ { "allele": "A", "end": 3133, "referenceAllele": "G", "start": 3132 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "NM_001291593.1:c.1636G>A" ], "proteinEffect": { "hgvs": "NP_001278522.1:p.Ala546Thr", "hgvsWellDefined": "NP_001278522.1:p.Ala546Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS024270" }, { "@id": "http://reg.genome.network/allele/PA916017813", "coordinates": [ { "allele": "A", "end": 2956, "referenceAllele": "G", "start": 2955 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "NM_001291594.1:c.1639G>A" ], "proteinEffect": { "hgvs": "NP_001278523.1:p.Ala547Thr", "hgvsWellDefined": "NP_001278523.1:p.Ala547Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS024271" }, { "@id": "http://reg.genome.network/allele/PA658811051", "coordinates": [ { "allele": "A", "end": 3443, "referenceAllele": "G", "start": 3442 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "NM_015102.4:c.3175G>A" ], "proteinEffect": { "hgvs": "NP_055917.1:p.Ala1059Thr", "hgvsWellDefined": "NP_055917.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS033743" }, { "coordinates": [ { "allele": "A", "end": 3990, "referenceAllele": "G", "start": 3989 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "NR_111987.1:n.3990G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS055173" }, { "coordinates": [ { "allele": "A", "end": 3462, "referenceAllele": "G", "start": 3461 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_006710563.2:c.3175G>A" ], "proteinEffect": { "hgvs": "XP_006710626.1:p.Ala1059Thr", "hgvsWellDefined": "XP_006710626.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS068685" }, { "coordinates": [ { "allele": "A", "end": 3672, "referenceAllele": "G", "start": 3671 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_006710565.2:c.3175G>A" ], "proteinEffect": { "hgvs": "XP_006710628.1:p.Ala1059Thr", "hgvsWellDefined": "XP_006710628.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS068686" }, { "coordinates": [ { "allele": "A", "end": 3210, "referenceAllele": "G", "start": 3209 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_011541213.1:c.3172G>A" ], "proteinEffect": { "hgvs": "XP_011539515.1:p.Ala1058Thr", "hgvsWellDefined": "XP_011539515.1:p.Ala1058Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS108156" }, { "coordinates": [ { "allele": "A", "end": 3171, "referenceAllele": "G", "start": 3170 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_011541214.1:c.3133G>A" ], "proteinEffect": { "hgvs": "XP_011539516.1:p.Ala1045Thr", "hgvsWellDefined": "XP_011539516.1:p.Ala1045Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS108157" }, { "coordinates": [ { "allele": "A", "end": 3102, "referenceAllele": "G", "start": 3101 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_011541215.1:c.3064G>A" ], "proteinEffect": { "hgvs": "XP_011539517.1:p.Ala1022Thr", "hgvsWellDefined": "XP_011539517.1:p.Ala1022Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS108158" }, { "coordinates": [ { "allele": "A", "end": 3910, "referenceAllele": "G", "start": 3909 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_011541216.1:c.3175G>A" ], "proteinEffect": { "hgvs": "XP_011539518.1:p.Ala1059Thr", "hgvsWellDefined": "XP_011539518.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS108159" }, { "coordinates": [ { "allele": "A", "end": 3774, "referenceAllele": "G", "start": 3773 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_011541217.1:c.3175G>A" ], "proteinEffect": { "hgvs": "XP_011539519.1:p.Ala1059Thr", "hgvsWellDefined": "XP_011539519.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS108160" }, { "coordinates": [ { "allele": "A", "end": 3440, "referenceAllele": "G", "start": 3439 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_011541218.1:c.3175G>A" ], "proteinEffect": { "hgvs": "XP_011539520.1:p.Ala1059Thr", "hgvsWellDefined": "XP_011539520.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS108161" }, { "coordinates": [ { "allele": "A", "end": 3615, "referenceAllele": "G", "start": 3614 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_011541219.1:c.3121G>A" ], "proteinEffect": { "hgvs": "XP_011539521.1:p.Ala1041Thr", "hgvsWellDefined": "XP_011539521.1:p.Ala1041Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS108162" }, { "coordinates": [ { "allele": "A", "end": 3213, "referenceAllele": "G", "start": 3212 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_011541220.1:c.3175G>A" ], "proteinEffect": { "hgvs": "XP_011539522.1:p.Ala1059Thr", "hgvsWellDefined": "XP_011539522.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS108163" }, { "coordinates": [ { "allele": "A", "end": 3082, "endIntronDirection": "+", "endIntronOffset": 347, "referenceAllele": "G", "start": 3082, "startIntronDirection": "+", "startIntronOffset": 346 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XR_946604.1:n.3082+347G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS140188" }, { "coordinates": [ { "allele": "A", "end": 3289, "referenceAllele": "G", "start": 3288 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_006710563.3:c.3175G>A" ], "proteinEffect": { "hgvs": "XP_006710626.1:p.Ala1059Thr", "hgvsWellDefined": "XP_006710626.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS537815" }, { "coordinates": [ { "allele": "A", "end": 3917, "referenceAllele": "G", "start": 3916 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_011541216.2:c.3175G>A" ], "proteinEffect": { "hgvs": "XP_011539518.1:p.Ala1059Thr", "hgvsWellDefined": "XP_011539518.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS554351" }, { "coordinates": [ { "allele": "A", "end": 3781, "referenceAllele": "G", "start": 3780 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_011541217.2:c.3175G>A" ], "proteinEffect": { "hgvs": "XP_011539519.1:p.Ala1059Thr", "hgvsWellDefined": "XP_011539519.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS554352" }, { "coordinates": [ { "allele": "A", "end": 3450, "referenceAllele": "G", "start": 3449 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_011541218.2:c.3175G>A" ], "proteinEffect": { "hgvs": "XP_011539520.1:p.Ala1059Thr", "hgvsWellDefined": "XP_011539520.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS554353" }, { "coordinates": [ { "allele": "A", "end": 3168, "referenceAllele": "G", "start": 3167 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_017000996.1:c.3130G>A" ], "proteinEffect": { "hgvs": "XP_016856485.1:p.Ala1044Thr", "hgvsWellDefined": "XP_016856485.1:p.Ala1044Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS557257" }, { "coordinates": [ { "allele": "A", "end": 3712, "referenceAllele": "G", "start": 3711 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_017000997.1:c.3175G>A" ], "proteinEffect": { "hgvs": "XP_016856486.1:p.Ala1059Thr", "hgvsWellDefined": "XP_016856486.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS557258" }, { "coordinates": [ { "allele": "A", "end": 3213, "referenceAllele": "G", "start": 3212 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_017000998.1:c.3175G>A" ], "proteinEffect": { "hgvs": "XP_016856487.1:p.Ala1059Thr", "hgvsWellDefined": "XP_016856487.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS557259" }, { "coordinates": [ { "allele": "A", "end": 3208, "referenceAllele": "G", "start": 3207 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_017000999.1:c.2647G>A" ], "proteinEffect": { "hgvs": "XP_016856488.1:p.Ala883Thr", "hgvsWellDefined": "XP_016856488.1:p.Ala883Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS557260" }, { "coordinates": [ { "allele": "A", "end": 3036, "referenceAllele": "G", "start": 3035 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_017001000.2:c.2647G>A" ], "proteinEffect": { "hgvs": "XP_016856489.1:p.Ala883Thr", "hgvsWellDefined": "XP_016856489.1:p.Ala883Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS557261" }, { "coordinates": [ { "allele": "A", "end": 2480, "referenceAllele": "G", "start": 2479 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_017001001.1:c.2377G>A" ], "proteinEffect": { "hgvs": "XP_016856490.1:p.Ala793Thr", "hgvsWellDefined": "XP_016856490.1:p.Ala793Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS557262" }, { "coordinates": [ { "allele": "A", "end": 2271, "referenceAllele": "G", "start": 2270 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XM_017001003.1:c.1636G>A" ], "proteinEffect": { "hgvs": "XP_016856492.1:p.Ala546Thr", "hgvsWellDefined": "XP_016856492.1:p.Ala546Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS557264" }, { "coordinates": [ { "allele": "A", "end": 3213, "referenceAllele": "G", "start": 3212 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XR_001737114.1:n.3213G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS587932" }, { "coordinates": [ { "allele": "A", "end": 3082, "endIntronDirection": "+", "endIntronOffset": 347, "referenceAllele": "G", "start": 3082, "startIntronDirection": "+", "startIntronOffset": 346 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "XR_001737115.1:n.3082+347G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS587933" }, { "@id": "http://reg.genome.network/allele/PA658811051", "coordinates": [ { "allele": "A", "end": 3395, "referenceAllele": "G", "start": 3394 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "NM_015102.5:c.3175G>A" ], "proteinEffect": { "hgvs": "NP_055917.1:p.Ala1059Thr", "hgvsWellDefined": "NP_055917.1:p.Ala1059Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS668638", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000378156.9:c.3175G>A" }, "RefSeq": { "hgvs": "NM_015102.5:c.3175G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000367398.4:p.Ala1059Thr" }, "RefSeq": { "hgvs": "NP_055917.1:p.Ala1059Thr" } } } }, { "@id": "http://reg.genome.network/allele/PA2826800569", "coordinates": [ { "allele": "A", "end": 3085, "referenceAllele": "G", "start": 3084 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "NM_001291593.2:c.1636G>A" ], "proteinEffect": { "hgvs": "NP_001278522.1:p.Ala546Thr", "hgvsWellDefined": "NP_001278522.1:p.Ala546Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS682839" }, { "@id": "http://reg.genome.network/allele/PA916017813", "coordinates": [ { "allele": "A", "end": 2908, "referenceAllele": "G", "start": 2907 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "NM_001291594.2:c.1639G>A" ], "proteinEffect": { "hgvs": "NP_001278523.1:p.Ala547Thr", "hgvsWellDefined": "NP_001278523.1:p.Ala547Thr" }, "referenceSequence": "http://reg.genome.network/refseq/RS682840" }, { "coordinates": [ { "allele": "A", "end": 3942, "referenceAllele": "G", "start": 3941 } ], "gene": "http://reg.genome.network/gene/GN019104", "geneNCBI_id": 261734, "geneSymbol": "NPHP4", "hgvs": [ "NR_111987.2:n.3942G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS703187" } ], "type": "nucleotide" }