Database of Pathogenic Variants

Variant Detail

Variant Information

ID: DPV: 810
Chromosome: 7
Gene
HGVS (GRCh37/hg19): NC_000007.13:g.107350577A>G
HGVS (GRCh38/hg38): NC_000007.14:g.107710132A>G
HGVS (RNA): NM_000441.1:c.2168A>G
HGVS (Protein): NP_000432.1:p.H723R
dbSNP: -
ClinGen Allele Registry: CA253307
Allele Frequency

Individual Information

ID

DPVS:207.1

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

Disease

Partial deafness
MedGen:C0018772

Phenotype

Zygosity

compound heterozygote

Allele Origin

unknown

Affected Status

yes

Sample Type

Analysis Type

Next-Generation Sequencing - Illumina/Solexa

Collection Method

research

Compound heterozygous variant(s)

Data Submitter

Comment

ID

DPVS:315.1

Clinical Significance

Pathogenic

Date Last Evaluated

2015-07-06

Clinical Significance Citation

Van Hauwe, P. Two frequent missense mutations in Pendred syndrome. 1998 Hum Mol Genet. 1998 Jul;7(7):1099-104. PMID:9618166

Tekin, M. Screening the SLC26A4 gene in probands with deafness and goiter (Pendred syndrome) ascertained from a large group of students of the schools for the deaf in Turkey. 2003 Clin Genet. 2003 Oct;64(4):371-4. PMID:12974744

Reyes, S. Mutation analysis of SLC26A4 in mainland Chinese patients with enlarged vestibular aqueduct. 2009 Otolaryngol Head Neck Surg. 2009 Oct;141(4):502-8. doi: 10.1016/j.otohns.2009.07.004. PMID:19786220

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:1570.1

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

Asakura, Y. A patient with Pendred syndrome whose goiter progressed with normal serum thyrotropin and iodine organification. 2010 Am J Med Genet A. 2010 Jul;152A(7):1793-7. doi: 10.1002/ajmg.a.33456. PMID:20583162

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

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

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

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

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

ID

DPVS:7440.1

Clinical Significance

Pathogenic

Date Last Evaluated

2019-03-28

Clinical Significance Citation

Hosoya, M. Cochlear Cell Modeling Using Disease-Specific iPSCs Unveils a Degenerative Phenotype and Suggests Treatments for Congenital Progressive Hearing Loss. 2017 Cell Rep. 2017 Jan 3;18(1):68-81. doi: 10.1016/j.celrep.2016.12.020. PMID:28052261

Transcript

Disease

Dizygotic twins
OMIM:276400
MedGen:C0220761

Phenotype

Zygosity

homozygote

Allele Origin

germline

Affected Status

yes

Sample Type

Analysis Type

SEQuencing

Collection Method

literature only

Compound heterozygous variant(s)

Data Submitter

Comment

ID

DPVS:7441.1

Clinical Significance

Pathogenic

Date Last Evaluated

2019-03-28

Clinical Significance Citation

Transcript

Disease

Dizygotic twins
OMIM:276400
MedGen:C0220761

Phenotype

Zygosity

compound heterozygote

Allele Origin

germline

Affected Status

yes

Sample Type

Analysis Type

SEQuencing

Collection Method

literature only

Compound heterozygous variant(s)

Data Submitter

Comment

c.439A>G(;)2168A>G

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	107350577	NC_000007.13:g.107350577A>G	A	G	.	.	EXAC_AF=0.0001236;EXAC_AC=15;EXAC_AN=121406;GNOMAD_AF=0.00011938;GNOMAD_AC=30;GNOMAD_AN=251294;TOMMO_4_7K_AF=0.0024;TOMMO_4_7K_AC=23;TOMMO_4_7K_AN=9544;CLNALLELEID=19864;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/Likely_pathogenic;CLNHGVS=NC_000007.13:g.107350577A>G;HGVD_AAF=0.002066;HGVD_NR=2415;HGVD_AC=5;GENEINFO=8818:5172;DPVID=810;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:600791|OMIM:276400;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_4|Dizygotic_twins;DPVHGVS=NC_000007.13:g.107350577A>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-qd50s12y>
##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	107710132	NC_000007.13:g.107350577A>G	A	G	.	.	dbSNP_RSID=rs121908362;GNOMAD_AF=0.00011938;GNOMAD_AC=30;GNOMAD_AN=251294;CLNALLELEID=19864;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/Likely_pathogenic;CLNHGVS=NC_000007.14:g.107710132A>G;GENEINFO=8818:5172;DPVID=810;DPVSIG=Pathogenic;DPVDSDBID=MedGen:C0018772|OMIM:600791|OMIM:276400;DPVDBN=Partial_deafness|Deafness\x2c_autosomal_recessive\x2c_4|Dizygotic_twins;DPVHGVS=NC_000007.14:g.107710132A>G	.