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

Germline classification:
Pathogenic/Likely pathogenic (11 submissions)
Last evaluated:
Jan 19, 2022
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:
RCV000005095.18

Allele description

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:
4

Condition(s)

Name:
Pendred syndrome (PDS)
Synonyms:
DEAFNESS WITH GOITER; HYPOTHYROIDISM, CONGENITAL, DUE TO DYSHORMONOGENESIS, 2B; THYROID DYSHORMONOGENESIS 2B; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010134; MedGen: C0271829; Orphanet: 705; OMIM: 274600

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000025271OMIM
no assertion criteria provided
Pathogenic
(Jul 1, 2008)
germlineliterature only

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

SCV000086786GeneReviews
no classification provided
not providedgermlineliterature only

SCV000267506Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center
criteria provided, single submitter

(ACMG Guidelines, 2015)
Likely pathogenic
(Mar 18, 2016)
germlinereference population

PubMed (2)
[See all records that cite these PMIDs]

SCV001163099Baylor Genetics
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenicgermlineclinical testing

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

SCV001194173Myriad Genetics, Inc.
criteria provided, single submitter

(Myriad Women's Health Autosomal Recessive and X-Linked Classification Criteria (2019))
Pathogenic
(Dec 4, 2019)
unknownclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Citation Link,

SCV001244768Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 6, 2021)
germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV001438729The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine
no assertion criteria provided
Pathogenic
(May 12, 2020)
inheritedclinical testing

SCV001459941Natera, Inc.
no assertion criteria provided
Pathogenic
(Sep 16, 2020)
germlineclinical testing

SCV002026975Genome-Nilou Lab
criteria provided, single submitter

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

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

SCV002074332Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)
Pathogenic
(Jan 19, 2022)
germlineclinical testing

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

Citation Link,

SCV003935252Molecular Diagnostics Lab, Nemours Children's Health, Delaware
criteria provided, single submitter

(ACMG Guidelines, 2015)
Pathogenic
(May 7, 2020)
maternal, unknownclinical testing

PubMed (5)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenonot providednot providednot providednot providednot providedclinical testing
not providedinheritedyes1not providednot provided1not providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, literature only
not providedunknownunknownnot providednot providednot providednot providednot providedclinical testing
not providedmaternalyes1not providednot provided1not providedclinical testing
not providedmaternalunknown1not providednot provided1not providedclinical testing
not providedunknownno1not providednot provided1not providedclinical testing
East Asiangermlineunknown2not providednot providednot providednot providedreference population

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 (15)

Details of each submission

From OMIM, SCV000025271.2

#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 GeneReviews, SCV000086786.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature onlynot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center, SCV000267506.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1East Asian2not providednot providedreference population PubMed (2)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided2not providednot providednot provided

From Baylor Genetics, SCV001163099.1

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

From Myriad Genetics, Inc., SCV001194173.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

NM_000441.1(SLC26A4):c.2168A>G(H723R) is classified as pathogenic in the context of Pendred syndrome. Sources cited for classification include the following: PMID 18310264, 24007330, 20826203 and 17718863. Classification of NM_000441.1(SLC26A4):c.2168A>G(H723R) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

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

From Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV001244768.2

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

Description

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with Pendred syndrome (MIM#274600). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 20301640). (I) 0200 - Variant is predicted to result in a missense amino acid change from histidine to arginine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (v2: 32 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (1 heterozygote, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated STAS domain (DECIPHER, Uniprot). (I) 0801 - This variant has very strong previous evidence of pathogenicity in unrelated individuals. It is prevalent in individuals with Asian descent with Pendred syndrome or deafness 4 with enlarged vestibular aqueduct (ClinVar, PMID: 20301640). (SP) 1102 - Strong phenotype match for this individual. (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

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

From The Core Laboratory in Medical Center of Clinical Research, Shanghai Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, SCV001438729.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritedyes1not providednot provided1not providednot providednot provided

From Natera, Inc., SCV001459941.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Genome-Nilou Lab, SCV002026975.1

#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 Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV002074332.1

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

Description

Variant summary: SLC26A4 c.2168A>G (p.His723Arg) results in a non-conservative amino acid change located in the STAS domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00012 in 251294 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in SLC26A4 causing Pendred Syndrome (0.00012 vs 0.0035), allowing no conclusion about variant significance. c.2168A>G has been reported in the literature in multiple individuals affected with Pendred Syndrome or hearing loss (e.g. Sagong_2012, Jung_2016). These data indicate that the variant is very likely to be associated with disease. Fifteen clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

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

From Molecular Diagnostics Lab, Nemours Children's Health, Delaware, SCV003935252.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing
(GTR000325510.3)
PubMed (5)
2not provided1not providednot providedclinical testing
(GTR000325510.3)
PubMed (5)
3not provided1not providednot providedclinical testing
(GTR000325510.3)
PubMed (5)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1maternalyes1bloodnot provided
(GTR000325510.3)
1not providednot providednot provided
2maternalunknown1bloodnot provided
(GTR000325510.3)
1not providednot providednot provided
3unknownno1bloodnot provided
(GTR000325510.3)
1not providednot providednot provided

Last Updated: Sep 16, 2024