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

Variant: NM_000441.1(SLC26A4):c.1363A>T (p.Ile455Phe)

CA132664

43507 (ClinVar)

Gene: SLC26A4
Condition: Pendred syndrome
Inheritance Mode: Autosomal recessive inheritance
Link to MONDO
UUID: 2b9fd19d-de91-41b2-a416-dc26fa5062e4
Approved on: 2018-09-28
Published on: 2019-07-17

HGVS expressions

NM_000441.1:c.1363A>T
NM_000441.1(SLC26A4):c.1363A>T (p.Ile455Phe)
NC_000007.14:g.107694642A>T
CM000669.2:g.107694642A>T
NC_000007.13:g.107335087A>T
CM000669.1:g.107335087A>T
NC_000007.12:g.107122323A>T
NG_008489.1:g.39008A>T
ENST00000265715.7:c.1363A>T
ENST00000460748.1:n.466A>T
ENST00000477350.5:n.210A>T
ENST00000480841.5:n.212A>T
ENST00000497446.5:n.378A>T
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Benign

Met criteria codes 2
PP3 BA1
Not Met criteria codes 3
PM5 PM1 PS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The filtering allele frequency of the p.Ile455Phe variant in the SLC26A4 gene is 3% (981/30778) of South Asian chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org; calculated by using inverse allele frequency at https://www.cardiodb.org/allelefrequencyapp/), which is a high frequency that is consistent with benign classification based on thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive hearing loss variants (BA1).
Met criteria codes
PP3
ILE is conserved through zebrafish. Conflicting lines of computational evidence but meets criteria as REVEL score is 0.89 which is greater or equal to criteria of 0.7.
BA1
BS1. Allele frequency is greater than 0.3 %, meets criteria based on gnomAD, ExAC and 1000 genomes. - ANDREA: I think this meets BA1 because the filtering allele frequency is 2.9% in ExAC. Changed to BA1.
Not Met criteria codes
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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