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.706C>G (p.Leu236Val)

CA132738

43565 (ClinVar)

Gene: SLC26A4
Condition: Pendred syndrome
Inheritance Mode: Autosomal recessive inheritance
UUID: f3b84ed4-48e1-4d17-8fda-a9bacc5d12b8

HGVS expressions

NM_000441.1:c.706C>G
NM_000441.1(SLC26A4):c.706C>G (p.Leu236Val)
NM_000441.2:c.706C>G
ENST00000265715.7:c.706C>G
NC_000007.14:g.107675050C>G
CM000669.2:g.107675050C>G
NC_000007.13:g.107315495C>G
CM000669.1:g.107315495C>G
NC_000007.12:g.107102731C>G
NG_008489.1:g.19416C>G

Likely Pathogenic

Met criteria codes 5
PM2_Supporting PM3_Strong PP1 PP4 PM5
Not Met criteria codes 13
BS2 BS4 BP3 BP7 BP5 PS3 PS4 PS2 PVS1 PP3 PM4 PM1 PM6

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The c.706C>G (p.Leu236Val) variant in SLC26A4 was identified in 0.026% (9/34592) of Latino chromosomes, which is a low enough frequency to apply PM2_Supporting based on the thresholds defined by the ClinGen Hearing Loss Expert Panel for autosomal recessive Pendred syndrome (PM2_Supporting; gnomad.broadinstitute.org). This variant has been detected in 1 proband with hearing loss in trans with a pathogenic variant, in 2 probands with hearing loss with a second pathogenic variant with phase unknown, and in the homozygous state in 1 proband with hearing loss (PM3_Strong; Partners Laboratory for Molecular Medicine internal data ClinVar SCV000060159.5, ARUP internal data ClinVar SCV000605149.1, Chinese PLA General Hospital internal data, Molecular Otolaryngology and Renal Research Laboratories internal data). A different pathogenic missense variant (p.Leu236Pro) has been previously identified at this codon of SLC26A4, which may indicate that this residue is critical to the function of the protein (PM5; ClinVar Variation ID 4817). The variant has been reported to segregate with hearing loss in two affected family members (PP1; Partners Laboratory for Molecular Medicine internal data ClinVar SCV000060159.5). At least one patient with a variant in this gene displayed features of hearing loss with temporal bone abnormality (PP4; Partners Laboratory for Molecular Medicine internal data ClinVar SCV000060159.5). Of note, this variant has been suggested to constitute a haplotype with c.200C>G (p.Thr67Ser), which the Hearing Loss Expert Panel has classified as likely benign. 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, PM5, PM2_Supporting, PP1, PP4.
Met criteria codes
PM2_Supporting
Present in 0.026% (9/34592) of Latino alleles in gnomAD v2.
PM3_Strong
Detected in trans with p.Thr99fs in a patient with hearing loss (Partners Laboratory for Molecular Medicine internal data, ClinVar SCV000060159.6). Also identified at ARUP in a patient with bilateral SNHL and an additional pathogenic variant with phase unknown (ClinVar SCV000605149.1). This patient had a negative MRI and CT with no abnormalities identified. Additionally, it was seen in the homozygous state in 1 patient with congenital hearing loss (Molecular Otolaryngology and Renal Research Laboratories internal data) and in the heterozygous state in 1 patient with congenital hearing loss who also carried c.919-2A>G (Chinese PLA General Hospital internal data).

PP1
Detected in trans with a frameshift variant in 1 proband (Partners Laboratory for Molecular Medicine internal data, ClinVar SCV000060159.6). It then segregated across five meioses to a distant relative, where it was found in homozygosity in two siblings with congenital hearing loss and a paternal family history of hearing loss.
PP4
Detected in 1 proband with hearing loss and temporal bone abnormality (Partners Laboratory for Molecular Medicine internal data, ClinVar SCV000060159.6).
PM5
PM5 was applied for p.Leu236Pro, which is classified as pathogenic by 10 clinical labs in ClinVar (Variation ID: 4817).
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
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
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
PS3
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
PS2
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
PP3
REVEL score 0.3. Only 2 mammals had Val at this site. May impact splicing.
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2020-09-22
Published on: 2020-09-24
The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. If you have questions about the information contained on this website, please see a health care professional.
¤ Powered by BCM's Genboree.