Database of Pathogenic Variants

Variant Detail

Variant Information

ID: DPV: 1317
Chromosome: 10
Gene
HGVS (GRCh37/hg19): NC_000010.10:g.73538009G>A
HGVS (GRCh38/hg38): NC_000010.11:g.71778252G>A
HGVS (RNA): NM_022124.5:c.5131G>A
HGVS (Protein): NP_071407.4:p.V1711I
dbSNP: -
ClinGen Allele Registry: CA245543
Allele Frequency

Individual Information

ID

DPVS:962.1

Clinical Significance

Pathogenic

Date Last Evaluated

2017-07-03

Clinical Significance Citation

Miyagawa, M. Prevalence and clinical features of hearing loss patients with CDH23 mutations: a large cohort study. 2012 PLoS One. 2012;7(8):e40366. doi: 10.1371/journal.pone.0040366. Epub 2012 Aug 10. PMID:22899989

Transcript

Disease

Deafness, autosomal recessive, 12
OMIM:601386
MedGen:C1832394

Phenotype

Zygosity

single heterozygote

Allele Origin

germline

Affected Status

yes

Sample Type

Analysis Type

SEQuencing

Collection Method

clinical testing

Compound heterozygous variant(s)

Data Submitter

Comment

ID

DPVS:1588.1

Clinical Significance

Pathogenic

Date Last Evaluated

2018-01-30

Clinical Significance Citation

Sakuma, N. An effective screening strategy for deafness in combination with a next-generation sequencing platform: a consecutive analysis. 2016 J Hum Genet. 2016 Mar;61(3):253-61. doi: 10.1038/jhg.2015.143. Epub 2016 Jan 14. PMID:26763877

Transcript

Disease

Phenotype

Zygosity

single heterozygote

Allele Origin

germline

Affected Status

yes

Sample Type

Analysis Type

Next-Generation Sequencing

Collection Method

literature only

Compound heterozygous variant(s)

Data Submitter

Comment

ID

DPVS:1831.1

Clinical Significance

Uncertain significance

Date Last Evaluated

2018-03-30

Clinical Significance Citation

Mizutari, K. High prevalence of CDH23 mutations in patients with congenital high-frequency sporadic or recessively inherited hearing loss. 2015 Orphanet J Rare Dis. 2015 May 13;10:60. doi: 10.1186/s13023-015-0276-z. PMID:25963016

Transcript

Disease

Phenotype

Zygosity

single heterozygote

Allele Origin

germline

Affected Status

yes

Sample Type

Analysis Type

SEQuencing

Collection Method

literature only

Compound heterozygous variant(s)

Data Submitter

Comment

ClinVar

Model Animals

VCF

VCF (GRCh37/hg19)

											##fileformat=VCFv4.0
##reference=GRCh37
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=EXAC_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from ExAC r1)">
##INFO=<ID=EXAC_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ExAC r1)">
##INFO=<ID=EXAC_FILTER,Number=1,Type=String,Description="calculated by self of overlapping values in field FILTER (from ExAC r1)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=HGVD_AAF,Number=A,Type=Float,Description="Alternative Allele Frequency(s) NA/(NR+NAtotal) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_AC,Number=A,Type=Integer,Description="number(s) of alternative allele(s) (from HGVD/DBexome20170802)">
##INFO=<ID=HGVD_NR,Number=1,Type=Integer,Description="number of reference allele (from HGVD/DBexome20170802)">
##INFO=<ID=TOMMO_4_7K_AC,Number=A,Type=Integer,Description="Allele count in genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AF,Number=A,Type=Float,Description="Allele frequency, for each ALT allele, in the same order as listed  (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=TOMMO_4_7K_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from ToMMo 4.7KJPN (20190826))">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
10	73538009	NC_000010.10:g.73538009G>A	G	A	.	.	EXAC_AF=0.0002974;EXAC_AC=36;EXAC_AN=121058;GNOMAD_AF=0.00030092;GNOMAD_AC=75;GNOMAD_AN=249232;TOMMO_4_7K_AF=0.0008;TOMMO_4_7K_AC=8;TOMMO_4_7K_AN=9546;CLNALLELEID=194583;CLNDN=Usher_syndrome_type_1D|Deafness,_autosomal_recessive_12|Usher_syndrome|not_provided;CLNDISDB=MONDO:MONDO:0010984,MedGen:C1832845,OMIM:601067|MONDO:MONDO:0011067,MedGen:C1832394,OMIM:601386|MONDO:MONDO:0019501,MeSH:D052245,MedGen:C0271097,OMIM:PS276900,Orphanet:ORPHA886|MedGen:CN517202;CLNSIG=Likely_benign;CLNHGVS=NC_000010.10:g.73538009G>A;HGVD_AAF=0.000826;HGVD_NR=2418;HGVD_AC=2;GENEINFO=13733:64072;DPVID=1317;DPVSIG=Pathogenic|Uncertain_significance;DPVDSDBID=OMIM:601386|OMIM:601067;DPVDBN=Deafness\x2c_autosomal_recessive\x2c_12|Usher_syndrome_1D/F;DPVHGVS=NC_000010.10:g.73538009G>A	.

VCF (GRCh38/hg38)

											##fileformat=VCFv4.0
##reference=GRCh38
##INFO=<ID=CLNALLELEID,Number=1,Type=Integer,Description="the ClinVar Allele ID">
##INFO=<ID=CLNDISDB,Number=.,Type=String,Description="Tag-value pairs of disease database name and identifier, e.g. OMIM:NNNNNN (from ClinVar)">
##INFO=<ID=CLNDN,Number=.,Type=String,Description="ClinVar's preferred disease name for the concept specified by disease identifiers in CLNDISDB (from ClinVar)">
##INFO=<ID=CLNHGVS,Number=.,Type=String,Description="Top-level (primary assembly, alt, or patch) HGVS expression.(from ClinVar)">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Clinical significance for this single variant (from ClinVar)">
##INFO=<ID=GNOMAD_AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed (from gnomAD v2.1.1 )">
##INFO=<ID=GNOMAD_AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes (from gnomAD v2.1.1 )">
##INFO=<ID=dbSNP_RSID,Number=1,Type=String,Description="dbSNP ID (from dbSNP b151 )">
##originalFile=</tmp/crossmap-input-pi2h9os2>
##targetRefGenome=</usr/lib64/python2.7/site-packages/transvar/transvar.download/hg38.fa>
##INFO=<ID=GENEINFO,Number=1,Type=String,Description="Pairs each of gene symbol:gene id. The gene symbol and id are delimited by a colon (:)">
##INFO=<ID=DPVID,Number=.,Type=String,Description="DPV Variant ID">
##INFO=<ID=DPVSIG,Number=.,Type=String,Description="Variant Clinical Significance">
##INFO=<ID=DPVDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=DPVDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=DPVHGVS,Number=.,Type=String,Description="Variant in HGVS.">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO
10	71778252	NC_000010.10:g.73538009G>A	G	A	.	.	dbSNP_RSID=rs181611778;GNOMAD_AF=0.00030092;GNOMAD_AC=75;GNOMAD_AN=249232;CLNALLELEID=194583;CLNDN=Usher_syndrome_type_1D|Deafness,_autosomal_recessive_12|Usher_syndrome|not_provided;CLNDISDB=MONDO:MONDO:0010984,MedGen:C1832845,OMIM:601067|MONDO:MONDO:0011067,MedGen:C1832394,OMIM:601386|MONDO:MONDO:0019501,MeSH:D052245,MedGen:C0271097,OMIM:PS276900,Orphanet:ORPHA886|MedGen:CN517202;CLNSIG=Likely_benign;CLNHGVS=NC_000010.11:g.71778252G>A;GENEINFO=13733:64072;DPVID=1317;DPVSIG=Pathogenic|Uncertain_significance;DPVDSDBID=OMIM:601386|OMIM:601067;DPVDBN=Deafness\x2c_autosomal_recessive\x2c_12|Usher_syndrome_1D/F;DPVHGVS=NC_000010.11:g.71778252G>A	.