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


Variant: NM_000441.2(SLC26A4):c.1708G>A (p.Val570Ile)

CA132675

43521 (ClinVar)

Gene: SLC26A4
Condition: Pendred syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: 24075c06-5af4-42e6-8a7e-ef7203a64602
Approved on: 2022-10-31
Published on: 2023-01-23

HGVS expressions

NM_000441.2:c.1708G>A
NM_000441.2(SLC26A4):c.1708G>A (p.Val570Ile)
NC_000007.14:g.107701101G>A
CM000669.2:g.107701101G>A
NC_000007.13:g.107341546G>A
CM000669.1:g.107341546G>A
NC_000007.12:g.107128782G>A
NG_008489.1:g.45467G>A
ENST00000644269.2:c.1708G>A
ENST00000644846.1:n.419G>A
ENST00000265715.7:c.1708G>A
ENST00000480841.5:n.557G>A
ENST00000492030.2:n.91-726G>A
NM_000441.1:c.1708G>A

Likely Pathogenic

Met criteria codes 3
PP4 PP3 PM3_Strong
Not Met criteria codes 21
PP1 PP2 BA1 PM4 PM1 PM5 PM6 PM2 BS4 BS1 BS2 BP7 BP5 BP3 BP2 BP4 BP1 PVS1 PS2 PS4 PS1

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.1708G>A variant in SLC26A4 is a missense variant predicted to cause the substitution of valine by isoleucine at amino acid 570 (p.Val570Ile). This variant is absent from gnomAD v2.1.1 (PM2_Supporting). The computations predictor REVEL gives a score of 0.547, which is neither above nor below the thresholds predicting a damaging or benign impact on SLC26A4 function. This variant is located at the first nucleotide of the exon and is heavily conserved in UCSC. Splice prediction analysis using MaxEntScan suggests an impact on splicing from the loss of the 3' consensus splice sequence (PP3). The c.1708G>A (p.Val570Ile) variant in SLC26A4 has also been detected in 3 different patients with hearing loss and the variant was found in trans with the pathogenic variant p.Leu117Phe.This variant has been detected in at least 3 individuals with Pendred syndrome. All of these individuals were compound heterozygous for the variant and a pathogenic or likely pathogenic variant confirmed in trans (3 PM3 points, PMID: 34170635, SCV000060111.6) (PM3_Strong). At least two probands with this variant displayed features of sensorineural hearing loss and enlarged vestibular aqueduct, a phenotype specific for Pendred syndrome (PMID: 34170635, SCV000060111.6) (PP4). In summary, this variant meets the criteria to be classified as likely pathogenic for autosomal recessive Pendred syndrome based on the ACMG/AMP criteria applied as specified by the ClinGen Hearing Loss VCEP: PM3_Strong, PM2_Supporting, PP3, PP4 (ClinGen Hearing Loss VCEP specifications version 2; 10/31/2022)
Met criteria codes
PP4
A proband (LMM internal data) with the variant presented with SNHL with EVA which meets guidelines to be classified with PP4 according to the HLVCEP-specified guidelines. For details on the proband, please see the PM3 classification.
PP3
The nucleotide is heavily conserved (all 100 vertebrates in UCSC have Valine at this position) and splicing predictors (including MaxEntScan) predict the loss of the 3' consensus splice sequence.
PM3_Strong
A 6 month old proband of Ashkenazi Jewish ancestry presented with congenital moderate mixed hearing loss. She was found to be a compound heterozygote for 2 variants in SLC26A4 (p.Val570Ile and p.Leu117Phe, which is classified as LP by the HL VCEP in ClinVar). The two variants were confirmed in trans by parental testing. This proband also had Heterozygous MYO15A: p.Ala2456Gly, POU3F4: p.Pro169Leu, EYA4: p.Gly473Val variants. This proband was scored with 1 point for PM3. (LMM Internal Data) A 20 year old proband of Ashkenazi jewish ancestry presented with profound SNHL with EVA and was found to have the same variants as the proband above also confirmed in trans by parental testing. This proband was also scored with 1 PM3 point. A proband presenting with NSHL and EAV was found to harbor the variant in trans with a hotspot Path. SLC26A4 variant c.919-2A>G (ClinVar ID:4840) d to have the same variants as the proband above also confirmed in trans by parental testing. This proband was also scored with 1 PM3 point. Total PM3 Points: 3 --> PM3_Strong
Not Met criteria codes
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
The highest population minor allele frequency in gnomAD v2.1.1 is 0.0007951 (8/10062 alleles) in the Askenazi Jewish population (PM2_Supporting, BS1, and BA1 are not met)
PM4
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
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
The highest population minor allele frequency in gnomAD v2.1.1 is 0.0007951 (8/10062 alleles) in the Askenazi Jewish population (PM2_Supporting, BS1, and BA1 are not met)
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
The highest population minor allele frequency in gnomAD v2.1.1 is 0.0007951 (8/10062 alleles) in the Askenazi Jewish population (PM2_Supporting, BS1, and BA1 are not met)
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PVS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
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
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