Variant Detail

Variant Information
ID
DPV: 962
Chromosome
13
Gene
HGVS (GRCh37/hg19)
NC_000013.10:g.20763341C>T
HGVS (GRCh38/hg38)
NC_000013.11:g.20189202C>T
HGVS (RNA)
NM_004004.5:c.380G>A
HGVS (Protein)
NP_003995.2:p.R127H
dbSNP
-
ClinGen Allele Registry
CA134966
Allele Frequency
Individual Information

ID
DPVS:723.1
Clinical Significance
Pathogenic
Date Last Evaluated
2017-03-30
Clinical Significance Citation
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
Estivill, X. Connexin-26 mutations in sporadic and inherited sensorineural deafness. 1998 Lancet. 1998 Feb 7;351(9100):394-8. doi: 10.1016/S0140-6736(97)11124-2. PMID:9482292
Roux, A. F. Molecular epidemiology of DFNB1 deafness in France. 2004 BMC Med Genet. 2004 Mar 6;5:5. doi: 10.1186/1471-2350-5-5. PMID:15070423

Transcript
-
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
-

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	20763341	NC_000013.10:g.20763341C>T	C	T	.	.	EXAC_AF=0.015;EXAC_AC=1863;EXAC_AN=121412;GNOMAD_AF=0.013892;GNOMAD_AC=3478;GNOMAD_AN=250364;TOMMO_4_7K_AF=0.001;TOMMO_4_7K_AC=10;TOMMO_4_7K_AN=9544;CLNALLELEID=53912;CLNDN=Progressive_sensorineural_hearing_impairment|Deafness,_autosomal_recessive_1A|Deafness,_autosomal_dominant_3a|Hystrix-like_ichthyosis_with_deafness|Nonsyndromic_hearing_loss_and_deafness|not_specified|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0000397,Human_Phenotype_Ontology:HP:0000406,Human_Phenotype_Ontology:HP:0000408,Human_Phenotype_Ontology:HP:0008592,Human_Phenotype_Ontology:HP:0008601,Human_Phenotype_Ontology:HP:0008617,MedGen:C1843156|MONDO:MONDO:0009076,MedGen:C2673759,OMIM:220290|MONDO:MONDO:0011103,MedGen:C2675750,OMIM:601544|MONDO:MONDO:0011245,MedGen:C1865234,OMIM:602540|MONDO:MONDO:0019497,MedGen:CN043648,Orphanet:ORPHA87884|MedGen:CN169374|MedGen:CN517202;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNHGVS=NC_000013.10:g.20763341C>T;HGVD_AAF=0.000413;HGVD_NR=2419;HGVD_AC=1;GENEINFO=4284:2706;DPVID=962;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772;DPVDBN=Partial_deafness;DPVHGVS=NC_000013.10:g.20763341C>T	.
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-kg2ci6h5>
##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	20189202	NC_000013.10:g.20763341C>T	C	T	.	.	dbSNP_RSID=rs111033196;GNOMAD_AF=0.013892;GNOMAD_AC=3478;GNOMAD_AN=250364;CLNALLELEID=53912;CLNDN=Progressive_sensorineural_hearing_impairment|Deafness,_autosomal_recessive_1A|Deafness,_autosomal_dominant_3a|Hystrix-like_ichthyosis_with_deafness|Nonsyndromic_hearing_loss_and_deafness|not_specified|not_provided;CLNDISDB=Human_Phenotype_Ontology:HP:0000397,Human_Phenotype_Ontology:HP:0000406,Human_Phenotype_Ontology:HP:0000408,Human_Phenotype_Ontology:HP:0008592,Human_Phenotype_Ontology:HP:0008601,Human_Phenotype_Ontology:HP:0008617,MedGen:C1843156|MONDO:MONDO:0009076,MedGen:C2673759,OMIM:220290|MONDO:MONDO:0011103,MedGen:C2675750,OMIM:601544|MONDO:MONDO:0011245,MedGen:C1865234,OMIM:602540|MONDO:MONDO:0019497,MedGen:CN043648,Orphanet:ORPHA87884|MedGen:CN169374|MedGen:CN517202;CLNSIG=Conflicting_interpretations_of_pathogenicity;CLNHGVS=NC_000013.11:g.20189202C>T;GENEINFO=4284:2706;DPVID=962;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772;DPVDBN=Partial_deafness;DPVHGVS=NC_000013.11:g.20189202C>T	.