Variant Detail

Variant Information
ID
DPV: 787
Chromosome
7
Gene
HGVS (GRCh37/hg19)
NC_000007.13:g.107323898A>G
HGVS (GRCh38/hg38)
NC_000007.14:g.107683453A>G
HGVS (RNA)
NM_000441.1:c.919-2A>G
HGVS (Protein)
dbSNP
-
ClinGen Allele Registry
CA261445
Allele Frequency
Individual Information

ID
DPVS:293.1
Clinical Significance
Pathogenic
Date Last Evaluated
2015-07-06
Clinical Significance Citation
Yin, A. The carrier rate and mutation spectrum of genes associated with hearing loss in South China hearing female population of childbearing age. 2013 BMC Med Genet. 2013 May 29;14:57. doi: 10.1186/1471-2350-14-57. PMID:23718755
Smith, R. J. H. Pendred Syndrome/Nonsyndromic Enlarged Vestibular Aqueduct 1993 PMID:20301640
Coucke, P. J. Identification of two different mutations in the PDS gene in an inbred family with Pendred syndrome. 1999 J Med Genet. 1999 Jun;36(6):475-7. PMID:10874637
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:1558.1
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
Tsukamoto, K. Distribution and frequencies of PDS (SLC26A4) mutations in Pendred syndrome and nonsyndromic hearing loss associated with enlarged vestibular aqueduct: a unique spectrum of mutations in Japanese. 2003 Eur J Hum Genet. 2003 Dec;11(12):916-22. doi: 10.1038/sj.ejhg.5201073. PMID:14508505
Iwasaki, S. Association of SLC26A4 mutations with clinical features and thyroid function in deaf infants with enlarged vestibular aqueduct. 2006 J Hum Genet. 2006;51(9):805-10. doi: 10.1007/s10038-006-0027-z. Epub 2006 Aug 19. PMID:16924389
Park, H. J. Origins and frequencies of SLC26A4 (PDS) mutations in east and south Asians: global implications for the epidemiology of deafness. 2003 J Med Genet. 2003 Apr;40(4):242-8. PMID:12676893
Smith, R. J. H. Pendred Syndrome/Nonsyndromic Enlarged Vestibular Aqueduct 1993 PMID:20301640
Hu, H. Molecular analysis of hearing loss associated with enlarged vestibular aqueduct in the mainland Chinese: a unique SLC26A4 mutation spectrum. 2007 J Hum Genet. 2007;52(6):492-7. doi: 10.1007/s10038-007-0139-0. Epub 2007 Apr 19. PMID:17443271

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
-

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
7	107323898	NC_000007.13:g.107323898A>G	A	G	.	.	EXAC_AF=0.0003048;EXAC_AC=37;EXAC_AN=121410;GNOMAD_AF=0.00035855;GNOMAD_AC=90;GNOMAD_AN=251010;TOMMO_4_7K_AF=0.0008;TOMMO_4_7K_AC=8;TOMMO_4_7K_AN=9544;CLNALLELEID=19879;CLNDN=Pendred_syndrome|Deafness,_autosomal_recessive_4,_with_enlarged_vestibular_aqueduct|Autosomal_recessive_nonsyndromic_deafness|not_provided|Rare_genetic_deafness;CLNDISDB=MONDO:MONDO:0010134,MedGen:C0271829,OMIM:274600,Orphanet:ORPHA705,SNOMED_CT:70348004|MONDO:MONDO:0010933,MedGen:C3538946,OMIM:600791|MONDO:MONDO:0019588,MedGen:C1846647,OMIM:607197,OMIM:PS220290,Orphanet:ORPHA90636|MedGen:CN517202|MedGen:CN826980,Orphanet:ORPHA96210;CLNSIG=Pathogenic;CLNHGVS=NC_000007.13:g.107323898A>G;HGVD_AAF=0.000413;HGVD_NR=2419;HGVD_AC=1;GENEINFO=8818:5172;DPVID=787;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:600791;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_4;DPVHGVS=NC_000007.13:g.107323898A>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-z_svqnl1>
##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
7	107683453	NC_000007.13:g.107323898A>G	A	G	.	.	dbSNP_RSID=rs111033313;GNOMAD_AF=0.00035855;GNOMAD_AC=90;GNOMAD_AN=251010;CLNALLELEID=19879;CLNDN=Pendred_syndrome|Deafness,_autosomal_recessive_4,_with_enlarged_vestibular_aqueduct|not_provided|Rare_genetic_deafness;CLNDISDB=MONDO:MONDO:0010134,MedGen:C0271829,OMIM:274600,Orphanet:ORPHA705,SNOMED_CT:70348004|MONDO:MONDO:0010933,MedGen:C3538946,OMIM:600791|MedGen:CN517202|MedGen:CN826980,Orphanet:ORPHA96210;CLNSIG=Pathogenic;CLNHGVS=NC_000007.14:g.107683453A>G;GENEINFO=8818:5172;DPVID=787;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:600791;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_4;DPVHGVS=NC_000007.14:g.107683453A>G	.