The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

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Variant: NM_000441.2(SLC26A4):c.845G>A (p.Cys282Tyr)

CA261440

43568 (ClinVar)

Gene: SLC26A4
Condition: Pendred syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 77c881dd-2f00-4636-a5ae-ac1cae285bee
Approved on: 2020-02-19
Published on: 2020-02-19

HGVS expressions

NM_000441.2:c.845G>A
NM_000441.2(SLC26A4):c.845G>A (p.Cys282Tyr)
NC_000007.14:g.107683281G>A
CM000669.2:g.107683281G>A
NC_000007.13:g.107323726G>A
CM000669.1:g.107323726G>A
NC_000007.12:g.107110962G>A
NG_008489.1:g.27647G>A
ENST00000644269.2:c.845G>A
ENST00000265715.7:c.845G>A
NM_000441.1:c.845G>A
More

Likely Pathogenic

Met criteria codes 5
PP3 PP4 PM3_Strong PM2 PS3_Supporting

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The p.Cys282Tyr variant in SLC26A4 is present in 0.0053% of European (non-Finnish) chromosomes by gnomAD v2.1.1, which is a low enough frequency to apply PM2 based on the thresholds defined by the ClinGen Hearing Loss expert Panel for autosomal recessive hearing loss (PM2). The REVEL computational prediction analysis tool produced a score of 0.719, which is above the threshold necessary to apply PP3. This variant has been detected in 3 probands with hearing loss. For all of the patients, a pathogenic or suspected-pathogenic variant was observed in trans (PM3_Strong, PMID:26969326, Partners LMM unpublished data SCV000060163.6, EGL Genetic Diagnostics unpublished data SCV000343642.4). At least one proband with this variant displayed features of sensorineural hearing loss and enlarged vestibular aqueduct, a phenotype specific for Pendred syndrome (PP4, PMID:26969326). Functional studies including fluorescence assays have demonstrated that this variant impacts protein function (PS3_Supporting; PMID:26752218). In summary, this variant meets criteria to be classified as likely pathogenic for autosomal recessive Pendred syndrome based on the ACMG/AMP criteria applied as specified by the Hearing Loss Expert Panel (PM3_Strong, PM2, PP3, PP4, PS3_Supporting).
Met criteria codes
PP3
Residue highly conserved (present in all mammals and primates in UCSC) No predicted effect on splicing REVEL score: 0.719
PP4
Proband from publication and internal LMM case both have hearing loss with EVA.
PM3_Strong
One proband from publication and another proband (LMM Internal Data) with progressive mixed hearing loss with EVA were found to harbor this variant. Both probands also harbored the c.1001+1G>A variant in SLC26A4 in trans. This aggregates to 2 PM3 points which leads to a PM3_Strong classification.

PM2
Present in 0.0053% (6/113490) of European (non-Finnish) chromosomes in gnomAD v 2.1.1 and in 0.0015% (1/64560) of European (non-Finnish) chromosomes in v3
PS3_Supporting
Halide-sensitive probe assay as specified in the HL paper suggests the SLC26A4 variant has reduced iodine influx compated to WT, control (empty vector), and benign variant.

Curation History
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