Variant Detail

Variant Information
ID
DPV: 964
Chromosome
13
Gene
HGVS (GRCh37/hg19)
NC_000013.10:g.20763421_20763422delAT
HGVS (GRCh38/hg38)
NC_000013.11:g.20189282_20189283delAT
HGVS (RNA)
NM_004004.5:c.299_300delAT
HGVS (Protein)
NP_003995.2:p.H100Rfs*14
dbSNP
-
ClinGen Allele Registry
CA261643
Allele Frequency
Individual Information

ID
DPVS:725.1
Clinical Significance
Pathogenic
Date Last Evaluated
2017-03-30
Clinical Significance Citation
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

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
-

ID
DPVS:1551.1
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
Wang, Y. C. Mutations of Cx26 gene (GJB2) for prelingual deafness in Taiwan. 2002 Eur J Hum Genet. 2002 Aug;10(8):495-8. doi: 10.1038/sj.ejhg.5200838. PMID:12111646
Gabriel, H. Mutations in the connexin26/GJB2 gene are the most common event in non-syndromic hearing loss among the German population. 2001 Hum Mutat. 2001 Jun;17(6):521-2. doi: 10.1002/humu.1138. PMID:11385713
Lin, D. Assessment of denaturing high-performance liquid chromatography (DHPLC) in screening for mutations in connexin 26 (GJB2). 2001 Hum Mutat. 2001;18(1):42-51. doi: 10.1002/humu.1148. PMID:11438992
Abe, S. Prevalent connexin 26 gene (GJB2) mutations in Japanese. 2000 J Med Genet. 2000 Jan;37(1):41-3. PMID:10633133

Transcript
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Disease

Phenotype
-
Zygosity
single 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:7450.1
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	20763420	NC_000013.10:g.20763421_20763422delAT	CAT	C	.	.	EXAC_AF=4.118e-05;EXAC_AC=5;EXAC_AN=121412;GNOMAD_AF=6.3752e-05;GNOMAD_AC=16;GNOMAD_AN=250972;TOMMO_4_7K_AF=0.0006;TOMMO_4_7K_AC=6;TOMMO_4_7K_AN=9544;CLNALLELEID=53903;CLNDN=Deafness,_autosomal_recessive_1A|Deafness,_autosomal_recessive_1b|not_specified|not_provided|Rare_genetic_deafness;CLNDISDB=MONDO:MONDO:0009076,MedGen:C2673759,OMIM:220290|MONDO:MONDO:0012977,MedGen:C2675235,OMIM:612645|MedGen:CN169374|MedGen:CN517202|MedGen:CN826980,Orphanet:ORPHA96210;CLNSIG=Pathogenic;CLNHGVS=NC_000013.10:g.20763421_20763422del;HGVD_AAF=0.000826;HGVD_NR=2418;HGVD_AC=2;GENEINFO=4284:2706;DPVID=964;DPVSIG=Pathogenic;DPVDSDBID=OMIM:220290;DPVDBN=Deafness\x2c_autosomal_recessive\x2c_1A;DPVHGVS=NC_000013.10:g.20763421_20763422delAT	.
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-7navyyed>
##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	20189281	NC_000013.10:g.20763421_20763422delAT	CAT	C	.	.	dbSNP_RSID=rs111033204;GNOMAD_AF=6.3752e-05;GNOMAD_AC=16;GNOMAD_AN=250972;CLNALLELEID=53903;CLNDN=Deafness,_autosomal_recessive_1A|Deafness,_autosomal_recessive_1b|not_specified|not_provided|Rare_genetic_deafness;CLNDISDB=MONDO:MONDO:0009076,MedGen:C2673759,OMIM:220290|MONDO:MONDO:0012977,MedGen:C2675235,OMIM:612645|MedGen:CN169374|MedGen:CN517202|MedGen:CN826980,Orphanet:ORPHA96210;CLNSIG=Pathogenic;CLNHGVS=NC_000013.11:g.20189282_20189283del;GENEINFO=4284:2706;DPVID=964;DPVSIG=Pathogenic;DPVDSDBID=OMIM:220290;DPVDBN=Deafness\x2c_autosomal_recessive\x2c_1A;DPVHGVS=NC_000013.11:g.20189282_20189283delAT	.