Database of Pathogenic Variants - Variant Detail

Variant Detail

Variant Information

ID: DPV: 780
Chromosome: 7
Gene
HGVS (GRCh37/hg19): NC_000007.13:g.107314608G>A
HGVS (GRCh38/hg38): NC_000007.14:g.107674163G>A
HGVS (RNA): NM_000441.1:c.416-1G>A
HGVS (Protein)
dbSNP: -
ClinGen Allele Registry: CA16041102
Allele Frequency

Individual Information

DPVS:287.1
DPVS:1606.1

ID

DPVS:287.1

Clinical Significance

Pathogenic

Date Last Evaluated

2015-07-06

Clinical Significance Citation

Palos, F. Pendred syndrome in two Galician families: insights into clinical phenotypes through cellular, genetic, and molecular studies. 2008 J Clin Endocrinol Metab. 2008 Jan;93(1):267-77. doi: 10.1210/jc.2007-0539. Epub 2007 Oct 16. PMID:17940114

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

DNA

Analysis Type

SEQuencing

Collection Method

clinical testing

Compound heterozygous variant(s)

Data Submitter

Comment

-

ID

DPVS:1606.1

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

Miyagawa, M. Mutation spectrum and genotype-phenotype correlation of hearing loss patients caused by SLC26A4 mutations in the Japanese: a large cohort study. 2014 J Hum Genet. 2014 May;59(5):262-8. doi: 10.1038/jhg.2014.12. Epub 2014 Mar 6. PMID:24599119

Snabboon, T. Two common and three novel PDS mutations in Thai patients with Pendred syndrome. 2007 J Endocrinol Invest. 2007 Dec;30(11):907-13. doi: 10.1007/BF03349236. PMID:18250610

Palos, F. Pendred syndrome in two Galician families: insights into clinical phenotypes through cellular, genetic, and molecular studies. 2008 J Clin Endocrinol Metab. 2008 Jan;93(1):267-77. doi: 10.1210/jc.2007-0539. Epub 2007 Oct 16. PMID:17940114

Pang, X. Mono-allelic mutations of SLC26A4 is over-presented in deaf patients with non-syndromic enlarged vestibular aqueduct. 2015 Int J Pediatr Otorhinolaryngol. 2015 Aug;79(8):1351-3. doi: 10.1016/j.ijporl.2015.06.009. Epub 2015 Jun 11. PMID:26100058

Transcript

-

Disease

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

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	107314608	NC_000007.13:g.107314608G>A	G	A	.	.	GNOMAD_AF=3.9768e-06;GNOMAD_AC=1;GNOMAD_AN=251458;CLNALLELEID=357530;CLNDN=Pendred_syndrome|not_provided;CLNDISDB=MONDO:MONDO:0010134,MedGen:C0271829,OMIM:274600,Orphanet:ORPHA705,SNOMED_CT:70348004|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000007.13:g.107314608G>A;GENEINFO=8818:5172;DPVID=780;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:600791;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_4;DPVHGVS=NC_000007.13:g.107314608G>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-xd0879ag>
##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	107674163	NC_000007.13:g.107314608G>A	G	A	.	.	dbSNP_RSID=rs1057516988;GNOMAD_AF=3.9768e-06;GNOMAD_AC=1;GNOMAD_AN=251458;CLNALLELEID=357530;CLNDN=Pendred_syndrome|not_provided;CLNDISDB=MONDO:MONDO:0010134,MedGen:C0271829,OMIM:274600,Orphanet:ORPHA705,SNOMED_CT:70348004|MedGen:CN517202;CLNSIG=Pathogenic;CLNHGVS=NC_000007.14:g.107674163G>A;GENEINFO=8818:5172;DPVID=780;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:600791;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_4;DPVHGVS=NC_000007.14:g.107674163G>A	.