rs369484751
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The ENST00000359271.4(SLC2A10):c.797G>A(p.Gly266Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,614,142 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G266V) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000359271.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SLC2A10 | NM_030777.4 | c.797G>A | p.Gly266Glu | missense_variant | 2/5 | ENST00000359271.4 | NP_110404.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SLC2A10 | ENST00000359271.4 | c.797G>A | p.Gly266Glu | missense_variant | 2/5 | 1 | NM_030777.4 | ENSP00000352216 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152262Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251052Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135710
GnomAD4 exome AF: 0.0000486 AC: 71AN: 1461880Hom.: 0 Cov.: 33 AF XY: 0.0000495 AC XY: 36AN XY: 727238
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74390
ClinVar
Submissions by phenotype
Arterial tortuosity syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Sep 01, 2021 | This sequence change replaces glycine with glutamic acid at codon 266 of the SLC2A10 protein (p.Gly266Glu). The glycine residue is moderately conserved and there is a moderate physicochemical difference between glycine and glutamic acid. This variant is present in population databases (rs369484751, ExAC 0.002%). This variant has not been reported in the literature in individuals affected with SLC2A10-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at