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Variant: NM_000441.2(SLC26A4):c.1924T>C (p.Ser642Pro)

CA132685

43527 (ClinVar)

Gene: SLC26A4
Condition: Pendred syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: e93aa465-29e0-4b62-8b3a-75f3ae31260e
Approved on: 2022-10-31
Published on: 2023-01-23

HGVS expressions

NM_000441.2:c.1924T>C
NM_000441.2(SLC26A4):c.1924T>C (p.Ser642Pro)
NC_000007.14:g.107701947T>C
CM000669.2:g.107701947T>C
NC_000007.13:g.107342392T>C
CM000669.1:g.107342392T>C
NC_000007.12:g.107129628T>C
NG_008489.1:g.46313T>C
ENST00000644269.2:c.1924T>C
ENST00000644846.1:n.635T>C
ENST00000265715.7:c.1924T>C
ENST00000492030.2:n.211T>C
NM_000441.1:c.1924T>C
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Uncertain Significance

Met criteria codes 4
BS1 PP4 PP3 PM3_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Hearing Loss Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDH23, COCH, GJB2, KCNQ4, MYO6, MYO7A, SLC26A4, TECTA and USH2A Version 2

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.1924T>C variant in SLC26A4 is a missense variant predicted to cause the substitution of serine by proline at amino acid 642 (p.Ser642Pro). The highest population minor allele frequency in gnomAD v2.1.1 is 0.005308 (188/35420 alleles) in Latio/Admixed American population, which is higher than the ClinGen Hearing Loss VCEP threshold (>0.003) for BS1, and therefore meets this criterion (BS1). The computational predictor REVEL gives a score of 0.724, which is above the threshold of 0.7, evidence that correlates with impact to SLC26A4 function (PP3). This variant has been detected in at least one individual with Pendred syndrome who was reported to have a second pathogenic SLC26A4 variant with an unknown phase (0.5 PM3 points, SCV000060117.6.6) (PM3_Supporting). At least one proband with this variant displayed features of sensorineural hearing loss and enlarged vestibular aqueduct, a phenotype specific for Pendred syndrome (PP4, SCV000060117.6.6). In summary, due to conflicting evidence, this variant has been classified as uncertain for autosomal recessive Pendred syndrome based on the ACMG/AMP criteria applied as specified by the ClinGen Hearing Loss VCEP: BS1, PP3, PM3_Supporting, PP4 (ClinGen Hearing Loss VCEP specifications version 2; 10/31/2022).
Met criteria codes
BS1
The highest population minor allele frequency in gnomAD v2.1.1 is 0.005308 (188/35420 alleles) in Latio/Admixed American population, which is higher than the ClinGen Hearing Loss VCEP threshold (>0.003) for BS1, and therefore meets this criterion (BS1)
PP4
The variant was found in a Hispanic individual who had a second pathogenic SLC26A4 variant and was reported to have hearing loss with enlarged vestibular aqueduct (EVA). This was found in a ClinVar submission by LMM (Accession: SCV000060117.6).
PP3
REVEL score is 0.724, which meets the cutoff for PP3. The amino acid is relatively conserved but rat, dolphin, manatee and some other fish species have an alanine at this position. There is no predicted impact on splicing.
PM3_Supporting
This variant was found in one female individual with SNHL with EVA and she had another pathogenic variant in SLC26A4. The phase was not confirmed so it was given a score of 0.5 points for PM3 which meets criteria for PM3_Supporting.
Curation History
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