Variant Detail

Variant Information
ID
DPV: 965
Chromosome
13
Gene
HGVS (GRCh37/hg19)
NC_000013.10:g.20763488delG
HGVS (GRCh38/hg38)
NC_000013.11:g.20189349delG
HGVS (RNA)
NM_004004.5:c.235delC
HGVS (Protein)
NP_003995.2:p.L79Cfs*3
dbSNP
-
ClinGen Allele Registry
CA127025
Allele Frequency
Individual Information

ID
DPVS:726.1
Clinical Significance
Pathogenic
Date Last Evaluated
2017-03-30
Clinical Significance Citation
Abe, S. Prevalent connexin 26 gene (GJB2) mutations in Japanese. 2000 J Med Genet. 2000 Jan;37(1):41-3. PMID:10633133
Fuse, Y. Three novel connexin26 gene mutations in autosomal recessive non-syndromic deafness. 1999 Neuroreport. 1999 Jun 23;10(9):1853-7. PMID:10501520
Yao, J. A systematic review and meta-analysis of 235delC mutation of GJB2 gene. 2012 J Transl Med. 2012 Jul 2;10:136. doi: 10.1186/1479-5876-10-136. PMID:22747691
Lazarin, G. A. An empirical estimate of carrier frequencies for 400+ causal Mendelian variants: results from an ethnically diverse clinical sample of 23,453 individuals. 2013 Genet Med. 2013 Mar;15(3):178-86. doi: 10.1038/gim.2012.114. Epub 2012 Sep 13. PMID:22975760
Sagong, B. A rapid method for simultaneous screening of multi-gene mutations associated with hearing loss in the Korean population. 2013 PLoS One. 2013;8(3):e57237. doi: 10.1371/journal.pone.0057237. Epub 2013 Mar 1. PMID:23469187
Taniguchi, M. Carrier frequency of the GJB2 mutations that cause hereditary hearing loss in the Japanese population. 2015 J Hum Genet. 2015 Oct;60(10):613-7. doi: 10.1038/jhg.2015.82. Epub 2015 Jul 16. PMID:26178431
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
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Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
inherited
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
clinical testing
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:1549.1
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
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Disease

Phenotype
-
Zygosity
compound heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • Next-Generation Sequencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:7447.1
Clinical Significance
Pathogenic
Date Last Evaluated
2019-03-28
Clinical Significance Citation
Kasakura-Kimura, N. WFS1 and GJB2 mutations in patients with bilateral low-frequency sensorineural hearing loss. 2017 Laryngoscope. 2017 Sep;127(9):E324-E329. doi: 10.1002/lary.26528. Epub 2017 Mar 8. PMID:28271504

Transcript
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Disease

Phenotype
-
Zygosity
homozygote
Allele Origin
biparental
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:7449.1
Clinical Significance
Pathogenic
Date Last Evaluated
2019-03-28
Clinical Significance Citation
Kasakura-Kimura, N. WFS1 and GJB2 mutations in patients with bilateral low-frequency sensorineural hearing loss. 2017 Laryngoscope. 2017 Sep;127(9):E324-E329. doi: 10.1002/lary.26528. Epub 2017 Mar 8. PMID:28271504

Transcript
-
Disease

Phenotype
-
Zygosity
compound heterozygote
Allele Origin
germline
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
c.235delC(;)299_300delAT

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
13	20763487	NC_000013.10:g.20763488delG	GG	G	.	.	GENEINFO=4284:2706;DPVID=965;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:220290;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_1A;DPVHGVS=NC_000013.10:g.20763488delG	.
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-g0rd4_4a>
##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
13	20189348	NC_000013.10:g.20763488delG	GG	G	.	.	GENEINFO=4284:2706;DPVID=965;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:220290;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_1A;DPVHGVS=NC_000013.11:g.20189349delG	.