Database of Pathogenic Variants

Variant Detail

Variant Information

ID: DPV: 420
Chromosome: 10
Gene
HGVS (GRCh37/hg19): NC_000010.10:g.73464800G>A
HGVS (GRCh38/hg38): NC_000010.11:g.71705043G>A
HGVS (RNA): NM_001171930:c.2866G>A
HGVS (Protein): NP_001165401:p.E956K
dbSNP: -
ClinGen Allele Registry: CA5544361
Allele Frequency

Individual Information

ID

DPVS:321.1

Clinical Significance

Pathogenic

Date Last Evaluated

2015-07-06

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

Mori, K. Social Health Insurance-Based Simultaneous Screening for 154 Mutations in 19 Deafness Genes Efficiently Identified Causative Mutations in Japanese Hearing Loss Patients. 2016 PLoS One. 2016 Sep 14;11(9):e0162230. doi: 10.1371/journal.pone.0162230. eCollection 2016. PMID:27627659

Transcript

Disease

Partial deafness
MedGen:C0018772

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:590.1

Clinical Significance

Pathogenic

Date Last Evaluated

2017-03-30

Clinical Significance Citation

Moteki, H. Comprehensive genetic testing with ethnic-specific filtering by allele frequency in a Japanese hearing-loss population. 2016 Clin Genet. 2016 Apr;89(4):466-472. doi: 10.1111/cge.12677. Epub 2015 Oct 6. PMID:26346818

Transcript

Disease

Partial deafness
MedGen:C0018772

Phenotype

Zygosity

compound heterozygote

Allele Origin

inherited

Affected Status

yes

Sample Type

Analysis Type

Next-Generation Sequencing - Illumina/Solexa

Collection Method

research

Compound heterozygous variant(s)

Data Submitter

Comment

ID

DPVS:1578.1

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

compound 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:1816.1

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

compound 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	73464800	NC_000010.10:g.73464800G>A	G	A	.	.	EXAC_AF=3.31e-05;EXAC_AC=4;EXAC_AN=120846;EXAC_FILTER=VQSRTrancheSNP99.60to99.80;GNOMAD_AF=3.2488e-05;GNOMAD_AC=8;GNOMAD_AN=246242;TOMMO_4_7K_AF=0.0002;TOMMO_4_7K_AC=2;TOMMO_4_7K_AN=9546;CLNALLELEID=437859;CLNDN=Sensorineural_hearing_loss|Deafness,_autosomal_recessive_12|Autosomal_recessive_nonsyndromic_deafness|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0000374,Human_Phenotype_Ontology:HP:0000407,Human_Phenotype_Ontology:HP:0001753,Human_Phenotype_Ontology:HP:0001916,Human_Phenotype_Ontology:HP:0008538,Human_Phenotype_Ontology:HP:0008553,Human_Phenotype_Ontology:HP:0008565,Human_Phenotype_Ontology:HP:0008576,Human_Phenotype_Ontology:HP:0008611,Human_Phenotype_Ontology:HP:0008613,Human_Phenotype_Ontology:HP:0008614,MONDO:MONDO:0020678,MeSH:D006319,MedGen:C0018784,SNOMED_CT:60700002|MONDO:MONDO:0011067,MedGen:C1832394,OMIM:601386|MONDO:MONDO:0019588,MedGen:C1846647,OMIM:607197,OMIM:PS220290,Orphanet:ORPHA90636|MedGen:CN517202;CLNSIG=Likely_pathogenic;CLNHGVS=NC_000010.10:g.73464800G>A;GENEINFO=13733:64072;DPVID=420;DPVSIG=Pathogenic|Uncertain_significance;DPVDSDBID=MedGen:C0018772|OMIM:601067;DPVDBN=Partial_deafness|Usher_syndrome_1D/F;DPVHGVS=NC_000010.10:g.73464800G>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-hbu_7_xg>
##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	71705043	NC_000010.10:g.73464800G>A	G	A	.	.	dbSNP_RSID=rs756147087;GNOMAD_AF=3.2488e-05;GNOMAD_AC=8;GNOMAD_AN=246242;CLNALLELEID=437859;CLNDN=Sensorineural_hearing_loss|Deafness,_autosomal_recessive_12|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0000374,Human_Phenotype_Ontology:HP:0000407,Human_Phenotype_Ontology:HP:0001753,Human_Phenotype_Ontology:HP:0001916,Human_Phenotype_Ontology:HP:0008538,Human_Phenotype_Ontology:HP:0008553,Human_Phenotype_Ontology:HP:0008565,Human_Phenotype_Ontology:HP:0008576,Human_Phenotype_Ontology:HP:0008611,Human_Phenotype_Ontology:HP:0008613,Human_Phenotype_Ontology:HP:0008614,MONDO:MONDO:0020678,MeSH:D006319,MedGen:C0018784,SNOMED_CT:60700002|MONDO:MONDO:0011067,MedGen:C1832394,OMIM:601386|MedGen:CN517202;CLNSIG=Likely_pathogenic;CLNHGVS=NC_000010.11:g.71705043G>A;GENEINFO=13733:64072;DPVID=420;DPVSIG=Pathogenic|Uncertain_significance;DPVDSDBID=MedGen:C0018772|OMIM:601067;DPVDBN=Partial_deafness|Usher_syndrome_1D/F;DPVHGVS=NC_000010.11:g.71705043G>A	.