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
Approved on: 2018-09-10
Published on: 2019-07-17

HGVS expressions

NM_000441.1:c.706C>G
NM_000441.1(SLC26A4):c.706C>G (p.Leu236Val)
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
ENST00000644269.2:c.706C>G
ENST00000265715.7:c.706C>G
NM_000441.2:c.706C>G
More

Likely Pathogenic

Met criteria codes 5
PP1 PP4 PM3 PM5 PM2_Supporting
Not Met criteria codes 21
PP2 PP3 PM6 PS1 PS2 PS3 PS4 PM1 PM4 BA1 PVS1 BP5 BP7 BP4 BP3 BP1 BP2 BS2 BS1 BS4 BS3

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Hearing Loss VCEP
The allele frequency of the p.Leu236Val variant in the SLC26A4 gene is 0.027% (9/33580) of Latino chromosomes by the Genome Aggregation Database (http://gnomad.broadinstitute.org), 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_P). This variant has been detected in 1 proband with hearing loss in trans with a pathogenic variant (PM3; Partners LMM internal data SCV000060159.5). 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 LMM internal data SCV000060159.5). At least one patient with a variant in this gene displayed features of hearing loss with temporal bone abnormality (PP4; Partners LMM internal data SCV000060159.5). 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: PM5, PM3, PM2_P, PP1, PP4.
Met criteria codes
PP1
For LMM case where it was detected in trans with a frameshift variant in the proband, 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
LMM proband has temporal bone abnormality. Gene/phenotype included on HL list for PP4
PM3
LMM case detected in trans with p.Thr99fs. Variant also identified at ARUP in a patient with bilateral SNHL and an additional pathogenic variant (unknown phase). Patient had a negative MRI and CT with no abnormalities identified.

PM5
p.Leu236Pro called pathogenic by four clinical labs in ClinVar
PM2_Supporting
gnomAD frequency of 0.027% in Latinos (9 alleles). Not low enough for PM2, but meets PM2_Supporting
Not Met criteria codes
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL score 0.3
PM6
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
PS2
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
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
gnomAD frequency of 0.027% in Latinos (9 alleles). Not low enough for PM2, but meets PM2_Supporting
PVS1
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
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
REVEL score 0.3
BP3
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
BP2
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
gnomAD frequency of 0.027% in Latinos (9 alleles). Not low enough for PM2, but meets PM2_Supporting
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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.