rs765749301
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_020451.3(SELENON):c.482G>A(p.Arg161Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000279 in 1,614,082 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Consequence
NM_020451.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SELENON | NM_020451.3 | c.482G>A | p.Arg161Gln | missense_variant | 4/13 | ENST00000361547.7 | |
SELENON | NM_206926.2 | c.380G>A | p.Arg127Gln | missense_variant | 3/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SELENON | ENST00000361547.7 | c.482G>A | p.Arg161Gln | missense_variant | 4/13 | 1 | NM_020451.3 | ||
SELENON | ENST00000374315.1 | c.380G>A | p.Arg127Gln | missense_variant | 3/12 | 5 | P1 | ||
SELENON | ENST00000354177.9 | c.380G>A | p.Arg127Gln | missense_variant | 3/12 | 5 | |||
SELENON | ENST00000494537.2 | c.380G>A | p.Arg127Gln | missense_variant, NMD_transcript_variant | 3/13 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249506Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135390
GnomAD4 exome AF: 0.0000294 AC: 43AN: 1461860Hom.: 1 Cov.: 34 AF XY: 0.0000303 AC XY: 22AN XY: 727232
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152222Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74364
ClinVar
Submissions by phenotype
Eichsfeld type congenital muscular dystrophy Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Feb 12, 2020 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jul 10, 2023 | This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 161 of the SELENON protein (p.Arg161Gln). This variant is present in population databases (rs765749301, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with SELENON-related conditions. ClinVar contains an entry for this variant (Variation ID: 373919). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt SELENON protein function. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
See cases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Jan 01, 2016 | This variant was classified as: Uncertain significance. - |
Pain;C0086437:Joint laxity;C0476403:EMG abnormality;C4021726:EMG: myopathic abnormalities Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Sep 23, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at