rs201905280
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 5P and 4B. PM1PM5PP3BP4_Strong
The NM_000441.2(SLC26A4):c.441G>A(p.Met147Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000244 in 1,614,126 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M147T) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000441.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SLC26A4 | NM_000441.2 | c.441G>A | p.Met147Ile | missense_variant | 5/21 | ENST00000644269.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SLC26A4 | ENST00000644269.2 | c.441G>A | p.Met147Ile | missense_variant | 5/21 | NM_000441.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000342 AC: 52AN: 152146Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000565 AC: 142AN: 251466Hom.: 1 AF XY: 0.000559 AC XY: 76AN XY: 135904
GnomAD4 exome AF: 0.000234 AC: 342AN: 1461862Hom.: 2 Cov.: 31 AF XY: 0.000230 AC XY: 167AN XY: 727234
GnomAD4 genome ? AF: 0.000342 AC: 52AN: 152264Hom.: 0 Cov.: 32 AF XY: 0.000443 AC XY: 33AN XY: 74452
ClinVar
Submissions by phenotype
Pendred syndrome Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Nov 14, 2017 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Molecular Diagnostics Lab, Nemours Children's Health, Delaware | May 18, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
not provided Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Oct 01, 2017 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 21, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Oct 05, 2021 | Identified in a patient with unilateral hearing loss and ipsilateral enlarged vestibular aqueduct in the literature (Jonard et al., 2010), but no second variant was identified; Identified in a patient with congenital hypothyroidism without hearing loss and in multiple patients with congenital hypothyroidism whose hearing status was not reported in the published literature (Fu et al., 2016; Makretskaya et al., 2018); however, a second variant was not identified and one case also had a homozygous variant in another gene; In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 27771369, 30245029, 26886089, 20621367, 30240412, 16570074, 20128824) - |
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Jan 12, 2016 | The p.Met147Ile variant in SLC26A4 has been reported in 1 individual with unilat eral hearing loss and enlargement of the vestibular aqueduct (EVA) who did not h ave a second SLC26A4 variant (Jonard 2010). This variant has also been identifie d in 0.5% (35/6614) of Finnish chromosomes by the Exome Aggregation Consortium ( ExAC, http://exac.broadinstitute.org; dbSNP rs201905280). Although this variant has been seen in the general population, its frequency is not high enough to rul e out a pathogenic role. Computational prediction tools and conservation analyse s suggest that the p.Met147Ile variant may impact the protein, though this infor mation is not predictive enough to determine pathogenicity. Two additional varia nts at this position (p.Met147Val and p.Met147Thr) have also previously been rep orted in individuals with hearing loss and EVA. The p.Met147Val variant has been reported in at least 5 individuals with hearing loss and EVA all of whom were c ompound heterozygous for a second pathogenic SLC26A4 variant, and functional stu dies suggest that protein function may be altered (Park 2005, Albert 2006, Yoon 2008, Ishihara 2010, Huang 2011). The p.Met147Thr variant has been observed in a t least 3 homozygous individuals with hearing loss and segregated with hearing l oss in 1 family (Albert 2006, Rebeh 2010). In summary, the clinical significance of the p.Met147Ile variant is uncertain. - |
Autosomal recessive nonsyndromic hearing loss 4 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genome-Nilou Lab | Sep 05, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at