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NM_000441.2(SLC26A4):c.2168A>G (p.His723Arg) AND Autosomal recessive nonsyndromic hearing loss 4

Germline classification:
Pathogenic (7 submissions)
Last evaluated:
Mar 16, 2024
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000005094.14

Allele description [Variation Report for NM_000441.2(SLC26A4):c.2168A>G (p.His723Arg)]

NM_000441.2(SLC26A4):c.2168A>G (p.His723Arg)

Genes:
LOC123956210:Sharpr-MPRA regulatory region 3291 [Gene]
SLC26A4:solute carrier family 26 member 4 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q22.3
Genomic location:
Preferred name:
NM_000441.2(SLC26A4):c.2168A>G (p.His723Arg)
HGVS:
  • NC_000007.14:g.107710132A>G
  • NG_008489.1:g.54498A>G
  • NM_000441.2:c.2168A>GMANE SELECT
  • NP_000432.1:p.His723Arg
  • NC_000007.13:g.107350577A>G
  • NM_000441.1:c.2168A>G
  • O43511:p.His723Arg
  • c.2168A>G
Protein change:
H723R; HIS723ARG
Links:
UniProtKB: O43511#VAR_007449; OMIM: 605646.0011; dbSNP: rs121908362
NCBI 1000 Genomes Browser:
rs121908362
Molecular consequence:
  • NM_000441.2:c.2168A>G - missense variant - [Sequence Ontology: SO:0001583]
Functional consequence:
loss_of_function_variant [Sequence Ontology: SO:0002054]
Observations:
7

Condition(s)

Name:
Autosomal recessive nonsyndromic hearing loss 4 (DFNB4)
Synonyms:
NEUROSENSORY NONSYNDROMIC RECESSIVE DEAFNESS 4; DEAFNESS, AUTOSOMAL RECESSIVE 4, WITH ENLARGED VESTIBULAR AQUEDUCT, DIGENIC; Nonsyndromic enlarged vestibular aqueduct (NSEVA); See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010933; MedGen: C3538946; Orphanet: 90636; OMIM: 600791

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000025270OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 2008)
germlineliterature only

PubMed (6)
[See all records that cite these PMIDs]

SCV000611824Division of Hearing and Balance Research, National Hospital Organization Tokyo Medical Center
criteria provided, single submitter

(Submitter's publication)
Pathogenic
(Jul 1, 2017)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV000902362Genetic Testing Center for Deafness, Department of Otolaryngology Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital
no assertion criteria provided
Likely pathogenic
(Feb 26, 2019)
inheritedcase-control

SCV000994909National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Aug 20, 2019)
inherited, germlineclinical testing, in vitro

PubMed (3)
[See all records that cite these PMIDs]

SCV002026974Genome-Nilou Lab
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Sep 5, 2021)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

SCV0020586973billion
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Jan 3, 2022)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

PMID:9618166,

SCV004201811Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(Mar 16, 2024)
unknownclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedinheritedyes47not providednot providedyescase-control, clinical testing
not providedgermlineyes23not providednot provided1not providedclinical testing, in vitro

Citations

PubMed

Non-syndromic hearing loss associated with enlarged vestibular aqueduct is caused by PDS mutations.

Usami S, Abe S, Weston MD, Shinkawa H, Van Camp G, Kimberling WJ.

Hum Genet. 1999 Feb;104(2):188-92.

PubMed [citation]
PMID:
10190331

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.

Tekin M, Akçayöz D, Comak E, Boğoçlu G, Duman T, Fitoz S, Ilhan I, Akar N.

Clin Genet. 2003 Oct;64(4):371-4. No abstract available.

PubMed [citation]
PMID:
12974744
See all PubMed Citations (10)

Details of each submission

From OMIM, SCV000025270.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (6)

Description

In 3 families with autosomal recessive deafness-4 with enlarged vestibular aqueduct (DFNB4; 600791), Usami et al. (1999) identified a 2168A-G transition in exon 19 of the SLC26A4 gene, causing a his723-to-arg (H723R) substitution. This mutation was found in homozygosity in 1 family and in compound heterozygosity in affected members of the other 2 families, who also carried a 2162C-T transition in exon 19 of the SLC26A4 gene, resulting in a thr721-to-met (T721M; 605646.0012) substitution.

Tekin et al. (2003) identified the H723R mutation in homozygous state in a Turkish patient with classic Pendred syndrome (PDS; 274600). They noted that the mutation had been identified in families from Japan and China in which affected members had sensorineural hearing loss and enlarged vestibular aqueduct without goiter. Tekin et al. (2003) suggested that the detection of the H723R mutation in Turkey reflected the migration of the Turkish people from central Asia more than 1,000 years ago.

In 2 sibs with enlarged vestibular aqueduct and an unrelated patient with Pendred syndrome, Tsukamoto et al. (2003) identified compound heterozygosity for the H723R and T721M mutations in the SLC26A4 gene, and concluded that the 2 conditions are part of a continuous spectrum of disease.

Among 26 Korean patients with DFNB4 with enlarged vestibular aqueduct (EVA), Park et al. (2005) found that the H723R mutation was the most common, accounting for 40% of the mutant alleles.

Among Chinese patients with DFNB4 with EVA, Wang et al. (2007) found that H723R was the second most common mutation, accounting for 9% of mutant alleles.

Using in vitro cellular expression studies, Yoon et al. (2008) demonstrated that the H723R mutant protein was retained in the endoplasmic reticulum, whereas wildtype pendrin reached the plasma membrane. The mutant protein showed significantly decreased Cl-/HCO3- exchange activity, but the defects could be rescued considerably by decreased temperature.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

From Division of Hearing and Balance Research, National Hospital Organization Tokyo Medical Center, SCV000611824.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided22not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided22not providednot providednot provided

From Genetic Testing Center for Deafness, Department of Otolaryngology Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital, SCV000902362.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided4not providedyescase-controlnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot provided4not provided7not provided

From National Institute of Sensory Organs, National Hospital Organization Tokyo Medical Center, SCV000994909.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)
2not providednot providednot providednot providedin vitro PubMed (3)

Description

in vitro experiment

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyesnot providednot providednot providednot providednot providednot providednot provided
2germlineyesnot providednot providedassert pathogenicitynot providednot providednot providednot provided

From Genome-Nilou Lab, SCV002026974.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenonot providednot providednot providednot providednot providednot providednot provided

From 3billion, SCV002058697.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000004825, PMID:9618166, PS1_S).A different missense change at the same codon has been reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000949741, PMID:19040761,24599119, PM5_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.933, 3CNET: 0.958, PP3_P). A missense variant is a common mechanism associated with Deafness (PP2_P). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000113, PM2_M). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot provided1not providednot providednot provided

From Baylor Genetics, SCV004201811.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Nov 3, 2024