Database of Pathogenic Variants - Variant Detail

Variant Detail

Variant Information

ID: DPV: 452
Chromosome: 13
Gene
HGVS (GRCh37/hg19): NC_000013.10:g.20763150A>G
HGVS (GRCh38/hg38): NC_000013.11:g.20189011A>G
HGVS (RNA): NM_004004:c.571T>C
HGVS (Protein): NP_003995:p.F191L
dbSNP: -
ClinGen Allele Registry: CA134989
Allele Frequency

Individual Information

DPVS:339.1
DPVS:719.1

ID

DPVS:339.1

Clinical Significance

Pathogenic

Date Last Evaluated

2015-07-06

Clinical Significance Citation

Hwa, H. L. Mutation spectrum of the connexin 26 (GJB2) gene in Taiwanese patients with prelingual deafness. 2003 Genet Med. 2003 May-Jun;5(3):161-5. doi: 10.1097/01.GIM.0000066796.11916.94. PMID:12792423

Dahl, H. H. The contribution of GJB2 mutations to slight or mild hearing loss in Australian elementary school children. 2006 J Med Genet. 2006 Nov;43(11):850-5. doi: 10.1136/jmg.2006.042051. Epub 2006 Jul 13. PMID:16840571

Dai, P. GJB2 mutation spectrum in 2,063 Chinese patients with nonsyndromic hearing impairment. 2009 J Transl Med. 2009 Apr 14;7:26. doi: 10.1186/1479-5876-7-26. PMID:19366456

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

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

Ohtsuka, A. GJB2 deafness gene shows a specific spectrum of mutations in Japan, including a frequent founder mutation. 2003 Hum Genet. 2003 Apr;112(4):329-33. doi: 10.1007/s00439-002-0889-x. Epub 2003 Jan 31. PMID:12560944

Transcript

-

Disease

Partial deafness
MedGen:C0018772

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

-

ID

DPVS:719.1

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

Ohtsuka, A. GJB2 deafness gene shows a specific spectrum of mutations in Japan, including a frequent founder mutation. 2003 Hum Genet. 2003 Apr;112(4):329-33. doi: 10.1007/s00439-002-0889-x. Epub 2003 Jan 31. PMID:12560944

Hwa, H. L. Mutation spectrum of the connexin 26 (GJB2) gene in Taiwanese patients with prelingual deafness. 2003 Genet Med. 2003 May-Jun;5(3):161-5. doi: 10.1097/01.GIM.0000066796.11916.94. PMID:12792423

Dahl, H. H. The contribution of GJB2 mutations to slight or mild hearing loss in Australian elementary school children. 2006 J Med Genet. 2006 Nov;43(11):850-5. doi: 10.1136/jmg.2006.042051. Epub 2006 Jul 13. PMID:16840571

Dai, P. GJB2 mutation spectrum in 2,063 Chinese patients with nonsyndromic hearing impairment. 2009 J Transl Med. 2009 Apr 14;7:26. doi: 10.1186/1479-5876-7-26. PMID:19366456

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

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	20763150	NC_000013.10:g.20763150A>G	A	G	.	.	EXAC_AF=0.0001483;EXAC_AC=18;EXAC_AN=121412;GNOMAD_AF=0.00014321;GNOMAD_AC=36;GNOMAD_AN=251376;TOMMO_4_7K_AF=0.0004;TOMMO_4_7K_AC=4;TOMMO_4_7K_AN=9546;CLNALLELEID=53927;CLNDN=Deafness,_autosomal_recessive_1A|Deafness,_autosomal_dominant_3a|Hearing_loss|not_specified|none_provided;CLNDISDB=MONDO:MONDO:0009076,MedGen:C2673759,OMIM:220290|MONDO:MONDO:0011103,MedGen:C2675750,OMIM:601544|MedGen:C3887873|MedGen:CN169374|MedGen:CN235283;CLNSIG=Uncertain_significance;CLNHGVS=NC_000013.10:g.20763150A>G;HGVD_AAF=0.001653;HGVD_NR=2416;HGVD_AC=4;GENEINFO=4284:2706;DPVID=452;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772;DPVDBN=Partial_deafness;DPVHGVS=NC_000013.10:g.20763150A>G	.

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-i39weyul>
##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	20189011	NC_000013.10:g.20763150A>G	A	G	.	.	dbSNP_RSID=rs397516878;GNOMAD_AF=0.00014321;GNOMAD_AC=36;GNOMAD_AN=251376;CLNALLELEID=53927;CLNDN=Deafness,_autosomal_recessive_1A|Deafness,_autosomal_dominant_3a|Hearing_loss|not_specified|none_provided;CLNDISDB=MONDO:MONDO:0009076,MedGen:C2673759,OMIM:220290|MONDO:MONDO:0011103,MedGen:C2675750,OMIM:601544|MedGen:C3887873|MedGen:CN169374|MedGen:CN235283;CLNSIG=Uncertain_significance;CLNHGVS=NC_000013.11:g.20189011A>G;GENEINFO=4284:2706;DPVID=452;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772;DPVDBN=Partial_deafness;DPVHGVS=NC_000013.11:g.20189011A>G	.