rs750242262
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM1BP4
The NM_000171.4(GLRA1):c.605G>A(p.Gly202Glu) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,613,840 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. G202R) has been classified as Uncertain significance.
Frequency
Consequence
NM_000171.4 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 |
---|---|---|---|---|---|---|---|
GLRA1 | NM_000171.4 | c.605G>A | p.Gly202Glu | missense_variant | 6/9 | ENST00000274576.9 | |
GLRA1 | NM_001146040.2 | c.605G>A | p.Gly202Glu | missense_variant | 6/9 | ||
GLRA1 | NM_001292000.2 | c.356G>A | p.Gly119Glu | missense_variant | 5/8 | ||
GLRA1 | XM_047417105.1 | c.653G>A | p.Gly218Glu | missense_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRA1 | ENST00000274576.9 | c.605G>A | p.Gly202Glu | missense_variant | 6/9 | 1 | NM_000171.4 | P4 | |
GLRA1 | ENST00000455880.2 | c.605G>A | p.Gly202Glu | missense_variant | 6/9 | 1 | A1 | ||
GLRA1 | ENST00000471351.2 | n.888G>A | non_coding_transcript_exon_variant | 6/8 | 1 | ||||
GLRA1 | ENST00000462581.6 | c.*363G>A | 3_prime_UTR_variant, NMD_transcript_variant | 5/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251486Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135918
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461690Hom.: 0 Cov.: 31 AF XY: 0.00000963 AC XY: 7AN XY: 727170
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74322
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.605G>A (p.G202E) alteration is located in exon 6 (coding exon 6) of the GLRA1 gene. This alteration results from a G to A substitution at nucleotide position 605, causing the glycine (G) at amino acid position 202 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Hereditary hyperekplexia Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Mar 01, 2023 | This sequence change replaces glycine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 202 of the GLRA1 protein (p.Gly202Glu). This variant is present in population databases (rs750242262, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with GLRA1-related conditions. ClinVar contains an entry for this variant (Variation ID: 532837). 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 GLRA1 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at