Database of Pathogenic Variants

Variant Detail

Variant Information

ID: DPV: 808
Chromosome: 7
Gene
HGVS (GRCh37/hg19): NC_000007.13:g.107350571C>T
HGVS (GRCh38/hg38): NC_000007.14:g.107710126C>T
HGVS (RNA): NM_000441.1:c.2162C>T
HGVS (Protein): NP_000432.1:p.T721M
dbSNP: -
ClinGen Allele Registry: CA253308
Allele Frequency

Individual Information

DPVS:313.1
DPVS:1569.1

ID

DPVS:313.1

Clinical Significance

Pathogenic

Date Last Evaluated

2015-07-06

Clinical Significance Citation

Smith, R. J. H. Pendred Syndrome/Nonsyndromic Enlarged Vestibular Aqueduct 1993 PMID:20301640

Lopez-Bigas, N. Identification of five new mutations of PDS/SLC26A4 in Mediterranean families with hearing impairment. 2001 Hum Mutat. 2001 Dec;18(6):548. doi: 10.1002/humu.1238. PMID:11748854

Chen, N. Mutation analysis of SLC26A4 for Pendred syndrome and nonsyndromic hearing loss by high-resolution melting. 2011 J Mol Diagn. 2011 Jul;13(4):416-26. doi: 10.1016/j.jmoldx.2011.03.003. Epub 2011 Apr 29. PMID:21704276

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

Partial deafness
MedGen:C0018772

Phenotype

Zygosity

single heterozygote

Allele Origin

germline

Affected Status

yes

Sample Type

Analysis Type

SEQuencing

Collection Method

clinical testing

Compound heterozygous variant(s)

Data Submitter

Comment

ID

DPVS:1569.1

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

Usami, S. Non-syndromic hearing loss associated with enlarged vestibular aqueduct is caused by PDS mutations. 1999 Hum Genet. 1999 Feb;104(2):188-92. PMID:10190331

Kahrizi, K. Identification of SLC26A4 gene mutations in Iranian families with hereditary hearing impairment. 2009 Eur J Pediatr. 2009 Jun;168(6):651-3. doi: 10.1007/s00431-008-0809-8. Epub 2008 Sep 24. PMID:18813951

Ishihara, K. Salicylate restores transport function and anion exchanger activity of missense pendrin mutations. 2010 Hear Res. 2010 Dec 1;270(1-2):110-8. doi: 10.1016/j.heares.2010.08.015. Epub 2010 Sep 6. PMID:20826203

Transcript

Disease

Deafness, autosomal recessive, 4
OMIM:600791
MedGen:C1863752

Phenotype

Zygosity

compound heterozygote

Allele Origin

germline

Affected Status

yes

Sample Type

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	107350571	NC_000007.13:g.107350571C>T	C	T	.	.	EXAC_AF=5.766e-05;EXAC_AC=7;EXAC_AN=121408;GNOMAD_AF=5.1741e-05;GNOMAD_AC=13;GNOMAD_AN=251252;TOMMO_4_7K_AF=0.0002;TOMMO_4_7K_AC=2;TOMMO_4_7K_AN=9544;CLNALLELEID=19865;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_000007.13:g.107350571C>T;GENEINFO=8818:5172;DPVID=808;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:600791;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_4;DPVHGVS=NC_000007.13:g.107350571C>T	.

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-l1g2tx1t>
##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	107710126	NC_000007.13:g.107350571C>T	C	T	.	.	dbSNP_RSID=rs121908363;GNOMAD_AF=5.1741e-05;GNOMAD_AC=13;GNOMAD_AN=251252;CLNALLELEID=19865;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.107710126C>T;GENEINFO=8818:5172;DPVID=808;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:600791;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_4;DPVHGVS=NC_000007.14:g.107710126C>T	.