Variant Detail

Variant Information
ID
DPV: 788
Chromosome
7
Gene
HGVS (GRCh37/hg19)
NC_000007.13:g.107323983G>A
HGVS (GRCh38/hg38)
NC_000007.14:g.107683538G>A
HGVS (RNA)
NM_000441.1:c.1001+1G>A
HGVS (Protein)
dbSNP
-
ClinGen Allele Registry
CA261396
Allele Frequency
Individual Information

ID
DPVS:294.1
Clinical Significance
Pathogenic
Date Last Evaluated
2015-07-06
Clinical Significance Citation
Coyle, B. Molecular analysis of the PDS gene in Pendred syndrome. 1998 Hum Mol Genet. 1998 Jul;7(7):1105-12. PMID:9618167
Smith, R. J. H. Pendred Syndrome/Nonsyndromic Enlarged Vestibular Aqueduct 1993 PMID:20301640
Fugazzola, L. Differential diagnosis between Pendred and pseudo-Pendred syndromes: clinical, radiologic, and molecular studies. 2002 Pediatr Res. 2002 Apr;51(4):479-84. doi: 10.1203/00006450-200204000-00013. PMID:11919333
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:1559.1
Clinical Significance
Pathogenic
Date Last Evaluated
2018-01-30
Clinical Significance Citation
Bruns, G. A. Report of the committee on the genetic constitution of chromosome 1. 1989 Cytogenet Cell Genet. 1989;51(1-4):67-90. doi: 10.1159/000132781. PMID:2676387
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
Madden, C. The influence of mutations in the SLC26A4 gene on the temporal bone in a population with enlarged vestibular aqueduct. 2007 Arch Otolaryngol Head Neck Surg. 2007 Feb;133(2):162-8. doi: 10.1001/archotol.133.2.162. PMID:17309986
Smith, R. J. H. Pendred Syndrome/Nonsyndromic Enlarged Vestibular Aqueduct 1993 PMID:20301640
Coyle, B. Molecular analysis of the PDS gene in Pendred syndrome. 1998 Hum Mol Genet. 1998 Jul;7(7):1105-12. PMID:9618167

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	107323983	NC_000007.13:g.107323983G>A	G	A	.	.	EXAC_AF=0.0001977;EXAC_AC=24;EXAC_AN=121400;GNOMAD_AF=0.00019578;GNOMAD_AC=49;GNOMAD_AN=250282;CLNALLELEID=19858;CLNDN=Pendred_syndrome|Deafness,_autosomal_recessive_4,_with_enlarged_vestibular_aqueduct|SLC26A4-Related_Disorders|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:CN239421|MedGen:CN517202|MedGen:CN826980,Orphanet:ORPHA96210;CLNSIG=Pathogenic;CLNHGVS=NC_000007.13:g.107323983G>A;GENEINFO=8818:5172;DPVID=788;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:600791;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_4;DPVHGVS=NC_000007.13:g.107323983G>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-dfs6a0iv>
##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	107683538	NC_000007.13:g.107323983G>A	G	A	.	.	dbSNP_RSID=rs80338849;GNOMAD_AF=0.00019578;GNOMAD_AC=49;GNOMAD_AN=250282;CLNALLELEID=19858;CLNDN=Pendred_syndrome|Deafness,_autosomal_recessive_4,_with_enlarged_vestibular_aqueduct|SLC26A4-Related_Disorders|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:CN239421|MedGen:CN517202|MedGen:CN826980,Orphanet:ORPHA96210;CLNSIG=Pathogenic;CLNHGVS=NC_000007.14:g.107683538G>A;GENEINFO=8818:5172;DPVID=788;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:600791;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_4;DPVHGVS=NC_000007.14:g.107683538G>A	.