rs121918408
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The ENST00000274576.9(GLRA1):c.896G>T(p.Arg299Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R299Q) has been classified as Pathogenic.
Frequency
Consequence
ENST00000274576.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GLRA1 | NM_000171.4 | c.896G>T | p.Arg299Leu | missense_variant | 7/9 | ENST00000274576.9 | NP_000162.2 | |
GLRA1 | NM_001146040.2 | c.896G>T | p.Arg299Leu | missense_variant | 7/9 | NP_001139512.1 | ||
GLRA1 | NM_001292000.2 | c.647G>T | p.Arg216Leu | missense_variant | 6/8 | NP_001278929.1 | ||
GLRA1 | XM_047417105.1 | c.944G>T | p.Arg315Leu | missense_variant | 7/9 | XP_047273061.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GLRA1 | ENST00000274576.9 | c.896G>T | p.Arg299Leu | missense_variant | 7/9 | 1 | NM_000171.4 | ENSP00000274576 | P4 | |
GLRA1 | ENST00000455880.2 | c.896G>T | p.Arg299Leu | missense_variant | 7/9 | 1 | ENSP00000411593 | A1 | ||
GLRA1 | ENST00000471351.2 | n.1179G>T | non_coding_transcript_exon_variant | 7/8 | 1 | |||||
GLRA1 | ENST00000462581.6 | c.*654G>T | 3_prime_UTR_variant, NMD_transcript_variant | 6/8 | 1 | ENSP00000430595 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Hyperekplexia 1 Pathogenic:2
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 22, 1994 | - - |
Pathogenic, no assertion criteria provided | curation | GeneReviews | Oct 04, 2012 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Mar 29, 2024 | Published functional studies demonstrate a damaging effect as R299L reduces agonist activity (PMID: 7925268, 7518444); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 28122427, 7518444, 9009272, 7826634, 8298642, 7925268) - |
Hereditary hyperekplexia Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Nov 24, 2023 | This sequence change replaces arginine, which is basic and polar, with leucine, which is neutral and non-polar, at codon 299 of the GLRA1 protein (p.Arg299Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with autosomal dominant hyperekplexia (PMID: 8298642; Invitae). This variant is also known as p.Arg271Leu. ClinVar contains an entry for this variant (Variation ID: 16060). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on GLRA1 protein function. Experimental studies have shown that this missense change affects GLRA1 function (PMID: 7518444). This variant disrupts the p.Arg299 amino acid residue in GLRA1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8298642, 8733061, 19073849, 28122427, 28138086). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at