{ "@context": "http://reg.genome.network/schema/allele.jsonld", "@id": "http://reg.genome.network/allele/CA261910280", "communityStandardTitle": [ "NM_021728.4(OTX2):c.458G>A (p.Ser153Asn)" ], "externalRecords": { "ClinVarAlleles": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/?term=1869257[alleleid]", "alleleId": 1869257, "preferredName": "NM_021728.4(OTX2):c.458G>A (p.Ser153Asn)" } ], "ClinVarVariations": [ { "@id": "http://www.ncbi.nlm.nih.gov/clinvar/variation/2141722", "RCV": [ "RCV003058693" ], "variationId": 2141722 } ], "MyVariantInfo_hg19": [ { "@id": "http://myvariant.info/v1/variant/chr14:g.57268889C>T?assembly=hg19", "id": "chr14:g.57268889C>T" } ], "MyVariantInfo_hg38": [ { "@id": "http://myvariant.info/v1/variant/chr14:g.56802171C>T?assembly=hg38", "id": "chr14:g.56802171C>T" } ], "dbSNP": [ { "@id": "http://www.ncbi.nlm.nih.gov/snp/1040844433", "rs": 1040844433 } ], "gnomAD_2": [ { "@id": "http://gnomad.broadinstitute.org/variant/14-57268889-C-T?dataset=gnomad_r2_1", "id": "14-57268889-C-T", "variant": "14:57268889 C / T" } ], "gnomAD_4": [ { "@id": "http://gnomad.broadinstitute.org/variant/14-56802171-C-T?dataset=gnomad_r4", "id": "14-56802171-C-T", "variant": "14:56802171 C / T" } ] }, "genomicAlleles": [ { "chromosome": "14", "coordinates": [ { "allele": "T", "end": 56802171, "referenceAllele": "C", "start": 56802170 } ], "hgvs": [ "NC_000014.9:g.56802171C>T", "CM000676.2:g.56802171C>T" ], "referenceGenome": "GRCh38", "referenceSequence": "http://reg.genome.network/refseq/RS000062" }, { "chromosome": "14", "coordinates": [ { "allele": "T", "end": 57268889, "referenceAllele": "C", "start": 57268888 } ], "hgvs": [ "NC_000014.8:g.57268889C>T", "CM000676.1:g.57268889C>T" ], "referenceGenome": "GRCh37", "referenceSequence": "http://reg.genome.network/refseq/RS000038" }, { "chromosome": "14", "coordinates": [ { "allele": "T", "end": 56338642, "referenceAllele": "C", "start": 56338641 } ], "hgvs": [ "NC_000014.7:g.56338642C>T" ], "referenceGenome": "NCBI36", "referenceSequence": "http://reg.genome.network/refseq/RS000014" }, { "coordinates": [ { "allele": "A", "end": 13296, "referenceAllele": "G", "start": 13295 } ], "hgvs": [ "NG_008204.1:g.13296G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS000946" }, { "coordinates": [ { "allele": "A", "end": 19523, "referenceAllele": "G", "start": 19522 } ], "hgvs": [ "NG_008204.2:g.19523G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS733317" } ], "transcriptAlleles": [ { "coordinates": [ { "allele": "A", "end": 650, "referenceAllele": "G", "start": 649 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000554845.2:c.458G>A" ], "proteinEffect": { "hgvs": "ENSP00000451357.2:p.Ser153Asn", "hgvsWellDefined": "ENSP00000451357.2:p.Ser153Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS826017" }, { "coordinates": [ { "allele": "A", "end": 741, "referenceAllele": "G", "start": 740 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000555804.2:c.434G>A" ], "proteinEffect": { "hgvs": "ENSP00000451272.2:p.Ser145Asn", "hgvsWellDefined": "ENSP00000451272.2:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS826029" }, { "coordinates": [ { "allele": "A", "end": 652, "referenceAllele": "G", "start": 651 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000685244.1:c.434G>A" ], "proteinEffect": { "hgvs": "ENSP00000508798.1:p.Ser145Asn", "hgvsWellDefined": "ENSP00000508798.1:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS829963" }, { "coordinates": [ { "allele": "A", "end": 690, "referenceAllele": "G", "start": 689 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000339475.10:c.434G>A" ], "proteinEffect": { "hgvs": "ENSP00000343819.5:p.Ser145Asn", "hgvsWellDefined": "ENSP00000343819.5:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS747822" }, { "coordinates": [ { "allele": "A", "end": 645, "referenceAllele": "G", "start": 644 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000408990.8:c.434G>A" ], "proteinEffect": { "hgvs": "ENSP00000386185.3:p.Ser145Asn", "hgvsWellDefined": "ENSP00000386185.3:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS754247" }, { "coordinates": [ { "allele": "A", "end": 707, "endIntronDirection": "+", "endIntronOffset": 74, "referenceAllele": "G", "start": 707, "startIntronDirection": "+", "startIntronOffset": 73 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000672125.1:c.360+74G>A" ], "proteinEffect": { "hgvs": "ENSP00000500744.1:n.360+74G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS773282" }, { "coordinates": [ { "allele": "A", "end": 745, "referenceAllele": "G", "start": 744 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000672264.2:c.458G>A" ], "proteinEffect": { "hgvs": "ENSP00000500115.1:p.Ser153Asn", "hgvsWellDefined": "ENSP00000500115.1:p.Ser153Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS773323", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000672264.2:c.458G>A" }, "RefSeq": { "hgvs": "NM_021728.4:c.458G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000500115.1:p.Ser153Asn" }, "RefSeq": { "hgvs": "NP_068374.1:p.Ser153Asn" } } } }, { "coordinates": [ { "allele": "A", "end": 724, "referenceAllele": "G", "start": 723 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000673035.1:c.434G>A" ], "proteinEffect": { "hgvs": "ENSP00000500061.1:p.Ser145Asn", "hgvsWellDefined": "ENSP00000500061.1:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS773576" }, { "coordinates": [ { "allele": "A", "end": 808, "referenceAllele": "G", "start": 807 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000673481.1:c.458G>A" ], "proteinEffect": { "hgvs": "ENSP00000500595.1:p.Ser153Asn", "hgvsWellDefined": "ENSP00000500595.1:p.Ser153Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS773699" }, { "coordinates": [ { "allele": "A", "end": 735, "referenceAllele": "G", "start": 734 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000339475.9:c.458G>A" ], "proteinEffect": { "hgvs": "ENSP00000343819.4:p.Ser153Asn", "hgvsWellDefined": "ENSP00000343819.4:p.Ser153Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS260879" }, { "coordinates": [ { "allele": "A", "end": 641, "referenceAllele": "G", "start": 640 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000408990.7:c.434G>A" ], "proteinEffect": { "hgvs": "ENSP00000386185.3:p.Ser145Asn", "hgvsWellDefined": "ENSP00000386185.3:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS281164" }, { "coordinates": [ { "allele": "A", "end": 569, "referenceAllele": "G", "start": 568 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000554559.5:c.*174G>A" ], "proteinEffect": { "hgvs": "ENSP00000450468.1:n.*174G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS370730" }, { "coordinates": [ { "allele": "A", "end": 474, "referenceAllele": "G", "start": 473 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000554788.5:c.*174G>A" ], "proteinEffect": { "hgvs": "ENSP00000474486.1:n.*174G>A" }, "referenceSequence": "http://reg.genome.network/refseq/RS370909" }, { "coordinates": [ { "allele": "A", "end": 650, "referenceAllele": "G", "start": 649 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000554845.1:c.458G>A" ], "proteinEffect": { "hgvs": "ENSP00000451357.1:p.Ser153Asn", "hgvsWellDefined": "ENSP00000451357.1:p.Ser153Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS370952" }, { "coordinates": [ { "allele": "A", "end": 843, "referenceAllele": "G", "start": 842 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000555006.5:c.434G>A" ], "proteinEffect": { "hgvs": "ENSP00000452336.1:p.Ser145Asn", "hgvsWellDefined": "ENSP00000452336.1:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS371083" }, { "coordinates": [ { "allele": "A", "end": 741, "referenceAllele": "G", "start": 740 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "ENST00000555804.1:c.434G>A" ], "proteinEffect": { "hgvs": "ENSP00000451272.1:p.Ser145Asn", "hgvsWellDefined": "ENSP00000451272.1:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS371729" }, { "@id": "http://reg.genome.network/allele/PA2826523842", "coordinates": [ { "allele": "A", "end": 718, "referenceAllele": "G", "start": 717 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NM_001270523.1:c.434G>A" ], "proteinEffect": { "hgvs": "NP_001257452.1:p.Ser145Asn", "hgvsWellDefined": "NP_001257452.1:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS020345" }, { "@id": "http://reg.genome.network/allele/PA2826524180", "coordinates": [ { "allele": "A", "end": 871, "referenceAllele": "G", "start": 870 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NM_001270524.1:c.434G>A" ], "proteinEffect": { "hgvs": "NP_001257453.1:p.Ser145Asn", "hgvsWellDefined": "NP_001257453.1:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS020346" }, { "@id": "http://reg.genome.network/allele/PA2826524466", "coordinates": [ { "allele": "A", "end": 665, "referenceAllele": "G", "start": 664 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NM_001270525.1:c.458G>A" ], "proteinEffect": { "hgvs": "NP_001257454.1:p.Ser153Asn", "hgvsWellDefined": "NP_001257454.1:p.Ser153Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS020347" }, { "@id": "http://reg.genome.network/allele/PA2580429633", "coordinates": [ { "allele": "A", "end": 742, "referenceAllele": "G", "start": 741 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NM_021728.3:c.458G>A" ], "proteinEffect": { "hgvs": "NP_068374.1:p.Ser153Asn", "hgvsWellDefined": "NP_068374.1:p.Ser153Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS037015" }, { "@id": "http://reg.genome.network/allele/PA2830351146", "coordinates": [ { "allele": "A", "end": 641, "referenceAllele": "G", "start": 640 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NM_172337.2:c.434G>A" ], "proteinEffect": { "hgvs": "NP_758840.1:p.Ser145Asn", "hgvsWellDefined": "NP_758840.1:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS042722" }, { "coordinates": [ { "allele": "A", "end": 566, "referenceAllele": "G", "start": 565 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NR_073034.1:n.566G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS052438" }, { "coordinates": [ { "allele": "A", "end": 489, "referenceAllele": "G", "start": 488 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NR_073036.1:n.489G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS052439" }, { "@id": "http://reg.genome.network/allele/PA2826523842", "coordinates": [ { "allele": "A", "end": 721, "referenceAllele": "G", "start": 720 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NM_001270523.2:c.434G>A" ], "proteinEffect": { "hgvs": "NP_001257452.1:p.Ser145Asn", "hgvsWellDefined": "NP_001257452.1:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS681043" }, { "@id": "http://reg.genome.network/allele/PA2826524180", "coordinates": [ { "allele": "A", "end": 874, "referenceAllele": "G", "start": 873 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NM_001270524.2:c.434G>A" ], "proteinEffect": { "hgvs": "NP_001257453.1:p.Ser145Asn", "hgvsWellDefined": "NP_001257453.1:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS681044" }, { "@id": "http://reg.genome.network/allele/PA2826524466", "coordinates": [ { "allele": "A", "end": 669, "referenceAllele": "G", "start": 668 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NM_001270525.2:c.458G>A" ], "proteinEffect": { "hgvs": "NP_001257454.1:p.Ser153Asn", "hgvsWellDefined": "NP_001257454.1:p.Ser153Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS681045" }, { "@id": "http://reg.genome.network/allele/PA2580429633", "coordinates": [ { "allele": "A", "end": 745, "referenceAllele": "G", "start": 744 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NM_021728.4:c.458G>A" ], "proteinEffect": { "hgvs": "NP_068374.1:p.Ser153Asn", "hgvsWellDefined": "NP_068374.1:p.Ser153Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS698443", "MANE": { "maneVersion": "1.3", "maneStatus": "MANE Select", "nucleotide": { "Ensembl": { "hgvs": "ENST00000672264.2:c.458G>A" }, "RefSeq": { "hgvs": "NM_021728.4:c.458G>A" } }, "protein": { "Ensembl": { "hgvs": "ENSP00000500115.1:p.Ser153Asn" }, "RefSeq": { "hgvs": "NP_068374.1:p.Ser153Asn" } } } }, { "@id": "http://reg.genome.network/allele/PA2830351146", "coordinates": [ { "allele": "A", "end": 645, "referenceAllele": "G", "start": 644 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NM_172337.3:c.434G>A" ], "proteinEffect": { "hgvs": "NP_758840.1:p.Ser145Asn", "hgvsWellDefined": "NP_758840.1:p.Ser145Asn" }, "referenceSequence": "http://reg.genome.network/refseq/RS700522" }, { "coordinates": [ { "allele": "A", "end": 569, "referenceAllele": "G", "start": 568 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NR_073034.2:n.569G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS702647" }, { "coordinates": [ { "allele": "A", "end": 493, "referenceAllele": "G", "start": 492 } ], "gene": "http://reg.genome.network/gene/GN008522", "geneNCBI_id": 5015, "geneSymbol": "OTX2", "hgvs": [ "NR_073036.2:n.493G>A" ], "referenceSequence": "http://reg.genome.network/refseq/RS702648" } ], "type": "nucleotide" }