Variant Detail

Variant Information
ID
DPV: 702
Chromosome
4
Gene
HGVS (GRCh37/hg19)
NC_000004.11:g.6304112G>A
HGVS (GRCh38/hg38)
NC_000004.12:g.6302385G>A
HGVS (RNA)
NM_006005.3:c.2590G>A
HGVS (Protein)
NP_005996.2:p.E864K
dbSNP
-
ClinGen Allele Registry
CA116903
Allele Frequency
Individual Information

ID
DPVS:161.1
Clinical Significance
Pathogenic
Date Last Evaluated
2017-03-30
Clinical Significance Citation
Moteki, H. Comprehensive genetic testing with ethnic-specific filtering by allele frequency in a Japanese hearing-loss population. 2016 Clin Genet. 2016 Apr;89(4):466-472. doi: 10.1111/cge.12677. Epub 2015 Oct 6. PMID:26346818

Transcript
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Disease

Phenotype
-
Zygosity
single heterozygote
Allele Origin
inherited
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • Next-Generation Sequencing - Illumina/Solexa
Collection Method
research
Compound heterozygous variant(s)
Data Submitter
Comment
-

ID
DPVS:282.1
Clinical Significance
Pathogenic
Date Last Evaluated
2015-07-06
Clinical Significance Citation
Tranebjaerg, L. WFS1-Related Disorders 1993 PMID:20301750
Fukuoka, H. Mutations in the WFS1 gene are a frequent cause of autosomal dominant nonsyndromic low-frequency hearing loss in Japanese. 2007 J Hum Genet. 2007;52(6):510-5. doi: 10.1007/s10038-007-0144-3. Epub 2007 May 11. PMID:17492394
Brownstein, Z. Targeted genomic capture and massively parallel sequencing to identify genes for hereditary hearing loss in Middle Eastern families. 2011 Genome Biol. 2011 Sep 14;12(9):R89. doi: 10.1186/gb-2011-12-9-r89. PMID:21917145
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

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:7444.1
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
single heterozygote
Allele Origin
de novo
Affected Status
yes
Sample Type
  • DNA
Analysis Type
  • SEQuencing
Collection Method
literature only
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
4	6304112	NC_000004.11:g.6304112G>A	G	A	.	.	CLNALLELEID=19565;CLNDN=Autosomal_dominant_nonsyndromic_deafness_6|Wolfram-like_syndrome,_autosomal_dominant|DFNA6/14/38_Nonsyndromic_Low-Frequency_Sensorineural_Hearing_Loss|not_provided|Rare_genetic_deafness;CLNDISDB=MONDO:MONDO:0010963,MedGen:C1833021,OMIM:600965|MONDO:MONDO:0013673,MedGen:C3280358,OMIM:614296,Orphanet:ORPHA411590|MedGen:CN184629|MedGen:CN517202|MedGen:CN826980,Orphanet:ORPHA96210;CLNSIG=Pathogenic/Likely_pathogenic;CLNHGVS=NC_000004.11:g.6304112G>A;GENEINFO=12762:7466;DPVID=702;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:600965;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_dominant\x2c_6;DPVHGVS=NC_000004.11:g.6304112G>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-wmh0u4f4>
##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
4	6302385	NC_000004.11:g.6304112G>A	G	A	.	.	dbSNP_RSID=rs74315205;CLNALLELEID=19565;CLNDN=Autosomal_dominant_nonsyndromic_deafness_6|Wolfram-like_syndrome,_autosomal_dominant|DFNA6/14/38_Nonsyndromic_Low-Frequency_Sensorineural_Hearing_Loss|not_provided|Rare_genetic_deafness;CLNDISDB=MONDO:MONDO:0010963,MedGen:C1833021,OMIM:600965|MedGen:C3280358,OMIM:614296,Orphanet:ORPHA411590|MedGen:CN184629|MedGen:CN517202|MedGen:CN826980,Orphanet:ORPHA96210;CLNSIG=Pathogenic/Likely_pathogenic;CLNHGVS=NC_000004.12:g.6302385G>A;GENEINFO=12762:7466;DPVID=702;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:600965;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_dominant\x2c_6;DPVHGVS=NC_000004.12:g.6302385G>A	.