Variant Detail

Variant Information
ID
DPV: 970
Chromosome
13
Gene
HGVS (GRCh37/hg19)
NC_000013.10:g.20763702G>A
HGVS (GRCh38/hg38)
NC_000013.11:g.20189563G>A
HGVS (RNA)
NM_004004.5:c.19C>T
HGVS (Protein)
NP_003995.2:p.Q7*
dbSNP
-
ClinGen Allele Registry
CA261641
Allele Frequency
Individual Information

ID
DPVS:734.1
Clinical Significance
Pathogenic
Date Last Evaluated
2017-03-30
Clinical Significance Citation
Pandya, A. Frequency and distribution of GJB2 (connexin 26) and GJB6 (connexin 30) mutations in a large North American repository of deaf probands. 2003 Genet Med. 2003 Jul-Aug;5(4):295-303. doi: 10.1097/01.GIM.0000078026.01140.68. PMID:12865758
Paz-y-Mino, C. Frequency of GJB2 and del(GJB6-D13S1830) mutations among an Ecuadorian mestizo population. 2014 Int J Pediatr Otorhinolaryngol. 2014 Oct;78(10):1648-54. doi: 10.1016/j.ijporl.2014.07.014. Epub 2014 Jul 21. PMID:25085072

Transcript
-
Disease

Hearing loss

Phenotype
-
Zygosity
single heterozygote
Allele Origin
germline
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	20763702	NC_000013.10:g.20763702G>A	G	A	.	.	GNOMAD_AF=8.0202e-06;GNOMAD_AC=2;GNOMAD_AN=249370;CLNALLELEID=53895;CLNDN=Deafness,_autosomal_recessive_1A|Inborn_genetic_diseases|Rare_genetic_deafness;CLNDISDB=MONDO:MONDO:0009076,MedGen:C2673759,OMIM:220290|MeSH:D030342,MedGen:C0950123|MedGen:CN826980,Orphanet:ORPHA96210;CLNSIG=Pathogenic/Likely_pathogenic;CLNHGVS=NC_000013.10:g.20763702G>A;GENEINFO=4284:2706;DPVID=970;DPVSIG=Pathogenic;DPVDSDBID=OMIM:220290;DPVDBN=Deafness\x2c_autosomal_recessive\x2c_1A;DPVHGVS=NC_000013.10:g.20763702G>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-qpz_z2wu>
##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	20189563	NC_000013.10:g.20763702G>A	G	A	.	.	dbSNP_RSID=rs111033451;GNOMAD_AF=8.0202e-06;GNOMAD_AC=2;GNOMAD_AN=249370;CLNALLELEID=53895;CLNDN=Deafness,_autosomal_recessive_1A|Inborn_genetic_diseases|Rare_genetic_deafness;CLNDISDB=MONDO:MONDO:0009076,MedGen:C2673759,OMIM:220290|MeSH:D030342,MedGen:C0950123|MedGen:CN826980,Orphanet:ORPHA96210;CLNSIG=Pathogenic/Likely_pathogenic;CLNHGVS=NC_000013.11:g.20189563G>A;GENEINFO=4284:2706;DPVID=970;DPVSIG=Pathogenic;DPVDSDBID=OMIM:220290;DPVDBN=Deafness\x2c_autosomal_recessive\x2c_1A;DPVHGVS=NC_000013.11:g.20189563G>A	.