Variant Detail

Variant Information
ID
DPV: 455
Chromosome
13
Gene
HGVS (GRCh37/hg19)
NC_000013.10:g.20763294G>A
HGVS (GRCh38/hg38)
NC_000013.11:g.20189155G>A
HGVS (RNA)
NM_004004:c.427C>T
HGVS (Protein)
NP_003995:p.R143W
dbSNP
-
ClinGen Allele Registry
CA172234
Allele Frequency
Individual Information

ID
DPVS:342.1
Clinical Significance
Pathogenic
Date Last Evaluated
2015-07-06
Clinical Significance Citation
Richards, C. S. ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. 2008 Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae. PMID:18414213
Smith, R. J. H. Nonsyndromic Hearing Loss and Deafness, DFNB1 1993 PMID:20301449
Snoeckx, R. L. GJB2 mutations and degree of hearing loss: a multicenter study. 2005 Am J Hum Genet. 2005 Dec;77(6):945-57. doi: 10.1086/497996. Epub 2005 Oct 19. PMID:16380907
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
Brobby, G. W. Connexin 26 R143W mutation associated with recessive nonsyndromic sensorineural deafness in Africa. 1998 N Engl J Med. 1998 Feb 19;338(8):548-50. doi: 10.1056/NEJM199802193380813. PMID:9471561

Transcript
-
Disease

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:721.1
Clinical Significance
Pathogenic
Date Last Evaluated
2017-03-30
Clinical Significance Citation
Richards, C. S. ACMG recommendations for standards for interpretation and reporting of sequence variations: Revisions 2007. 2008 Genet Med. 2008 Apr;10(4):294-300. doi: 10.1097/GIM.0b013e31816b5cae. PMID:18414213
Smith, R. J. H. Nonsyndromic Hearing Loss and Deafness, DFNB1 1993 PMID:20301449
Snoeckx, R. L. GJB2 mutations and degree of hearing loss: a multicenter study. 2005 Am J Hum Genet. 2005 Dec;77(6):945-57. doi: 10.1086/497996. Epub 2005 Oct 19. PMID:16380907
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
Brobby, G. W. Connexin 26 R143W mutation associated with recessive nonsyndromic sensorineural deafness in Africa. 1998 N Engl J Med. 1998 Feb 19;338(8):548-50. doi: 10.1056/NEJM199802193380813. PMID:9471561
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

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:1552.1
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
Abe, S. Prevalent connexin 26 gene (GJB2) mutations in Japanese. 2000 J Med Genet. 2000 Jan;37(1):41-3. PMID:10633133
Snoeckx, R. L. GJB2 mutations and degree of hearing loss: a multicenter study. 2005 Am J Hum Genet. 2005 Dec;77(6):945-57. doi: 10.1086/497996. Epub 2005 Oct 19. PMID:16380907
Smith, R. J. H. Nonsyndromic Hearing Loss and Deafness, DFNB1 1993 PMID:20301449

Transcript
-
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:7448.1
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
compound heterozygote
Allele Origin
paternal
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
Compound heterozygous variant(s)
Data Submitter
Comment
c.[109G>A];[427C>T]

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	20763294	NC_000013.10:g.20763294G>A	G	A	.	.	EXAC_AF=0.0001647;EXAC_AC=20;EXAC_AN=121412;GNOMAD_AF=0.00011557;GNOMAD_AC=29;GNOMAD_AN=250932;TOMMO_4_7K_AF=0.0006;TOMMO_4_7K_AC=6;TOMMO_4_7K_AN=9546;CLNALLELEID=32048;CLNDN=Hearing_impairment|Mutilating_keratoderma|Keratitis-ichthyosis-deafness_syndrome,_autosomal_dominant|Palmoplantar_keratoderma-deafness_syndrome|Knuckle_pads,_deafness_AND_leukonychia_syndrome|Deafness,_autosomal_recessive_1A|Deafness,_X-linked_2|Deafness,_autosomal_dominant_3a|Hystrix-like_ichthyosis_with_deafness|Nonsyndromic_hearing_loss_and_deafness|Hearing_loss|none_provided|not_provided|Rare_genetic_deafness;CLNDISDB=Human_Phenotype_Ontology:HP:0000365,Human_Phenotype_Ontology:HP:0000404,Human_Phenotype_Ontology:HP:0001728,Human_Phenotype_Ontology:HP:0001729,Human_Phenotype_Ontology:HP:0001754,Human_Phenotype_Ontology:HP:0008560,Human_Phenotype_Ontology:HP:0008563,MONDO:MONDO:0005365,MedGen:C1384666|MONDO:MONDO:0007422,MedGen:C0265964,OMIM:124500,Orphanet:ORPHA494,SNOMED_CT:24559001|MONDO:MONDO:0007850,MedGen:C0265336,OMIM:148210|MONDO:MONDO:0007852,MedGen:C1835672,OMIM:148350,Orphanet:ORPHA2202|MONDO:MONDO:0007866,MedGen:C0266004,OMIM:149200,Orphanet:ORPHA2698,SNOMED_CT:1271009|MONDO:MONDO:0009076,MedGen:C2673759,OMIM:220290|MONDO:MONDO:0010576,MedGen:C1844678,OMIM:304400,Orphanet:ORPHA383|MONDO:MONDO:0011103,MedGen:C2675750,OMIM:601544|MONDO:MONDO:0011245,MedGen:C1865234,OMIM:602540|MONDO:MONDO:0019497,MedGen:CN043648,Orphanet:ORPHA87884|MedGen:C3887873|MedGen:CN235283|MedGen:CN517202|MedGen:CN826980,Orphanet:ORPHA96210;CLNSIG=Pathogenic;CLNHGVS=NC_000013.10:g.20763294G>A;HGVD_AAF=0.000827;HGVD_NR=2416;HGVD_AC=2;GENEINFO=4284:2706;DPVID=455;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:220290;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_1A;DPVHGVS=NC_000013.10:g.20763294G>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-02131gym>
##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	20189155	NC_000013.10:g.20763294G>A	G	A	.	.	dbSNP_RSID=rs80338948;GNOMAD_AF=0.00011557;GNOMAD_AC=29;GNOMAD_AN=250932;CLNALLELEID=32048;CLNDN=Hearing_impairment|Mutilating_keratoderma|Keratitis-ichthyosis-deafness_syndrome,_autosomal_dominant|Palmoplantar_keratoderma-deafness_syndrome|Knuckle_pads,_deafness_AND_leukonychia_syndrome|Deafness,_autosomal_recessive_1A|Deafness,_autosomal_dominant_3a|Hystrix-like_ichthyosis_with_deafness|Nonsyndromic_hearing_loss_and_deafness|Deafness,_X-linked_2|Hearing_loss|none_provided|not_provided|Rare_genetic_deafness;CLNDISDB=Human_Phenotype_Ontology:HP:0000365,Human_Phenotype_Ontology:HP:0000404,Human_Phenotype_Ontology:HP:0001728,Human_Phenotype_Ontology:HP:0001729,Human_Phenotype_Ontology:HP:0001754,Human_Phenotype_Ontology:HP:0008560,Human_Phenotype_Ontology:HP:0008563,MONDO:MONDO:0005365,MedGen:C1384666|MONDO:MONDO:0007422,MedGen:C0265964,OMIM:124500,Orphanet:ORPHA494,SNOMED_CT:24559001|MONDO:MONDO:0007850,MedGen:C0265336,OMIM:148210|MONDO:MONDO:0007852,MedGen:C1835672,OMIM:148350,Orphanet:ORPHA2202|MONDO:MONDO:0007866,MedGen:C0266004,OMIM:149200,Orphanet:ORPHA2698,SNOMED_CT:1271009|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:C1844678,OMIM:304400|MedGen:C3887873|MedGen:CN235283|MedGen:CN517202|MedGen:CN826980,Orphanet:ORPHA96210;CLNSIG=Pathogenic;CLNHGVS=NC_000013.11:g.20189155G>A;GENEINFO=4284:2706;DPVID=455;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:220290;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_1A;DPVHGVS=NC_000013.11:g.20189155G>A	.