rs281864914
Variant summary
Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1PM5PP3_StrongPP5_Moderate
The NM_000171.4(GLRA1):c.299G>A(p.Arg100His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000026 in 1,613,932 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 13/21 in silico tools predict a damaging 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. R100C) has been classified as Pathogenic.
Frequency
Consequence
NM_000171.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRA1 | NM_000171.4 | c.299G>A | p.Arg100His | missense_variant | 4/9 | ENST00000274576.9 | |
GLRA1 | NM_001146040.2 | c.299G>A | p.Arg100His | missense_variant | 4/9 | ||
GLRA1 | NM_001292000.2 | c.50G>A | p.Arg17His | missense_variant | 3/8 | ||
GLRA1 | XM_047417105.1 | c.347G>A | p.Arg116His | missense_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRA1 | ENST00000274576.9 | c.299G>A | p.Arg100His | missense_variant | 4/9 | 1 | NM_000171.4 | P4 | |
GLRA1 | ENST00000455880.2 | c.299G>A | p.Arg100His | missense_variant | 4/9 | 1 | A1 | ||
GLRA1 | ENST00000471351.2 | n.582G>A | non_coding_transcript_exon_variant | 4/8 | 1 | ||||
GLRA1 | ENST00000462581.6 | c.*57G>A | 3_prime_UTR_variant, NMD_transcript_variant | 3/8 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251452Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135908
GnomAD4 exome AF: 0.0000280 AC: 41AN: 1461820Hom.: 0 Cov.: 32 AF XY: 0.0000234 AC XY: 17AN XY: 727210
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74298
ClinVar
Submissions by phenotype
Hyperekplexia 1 Pathogenic:1
Pathogenic, no assertion criteria provided | curation | GeneReviews | Oct 04, 2012 | - - |
Hereditary hyperekplexia Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jun 17, 2022 | 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. This variant disrupts the p.Arg100 amino acid residue in GLRA1. Other variant(s) that disrupt this residue have been observed in individuals with GLRA1-related conditions (PMID: 16078201, 24108130), which suggests that this may be a clinically significant amino acid residue. Experimental studies have shown that this missense change affects GLRA1 function (PMID: 25568133). 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 expected to disrupt GLRA1 protein function. ClinVar contains an entry for this variant (Variation ID: 38328). This variant is also known as p.R72H. This missense change has been observed in individual(s) with autosomal recessive hyperekplexia (PMID: 16078201). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs281864914, gnomAD 0.007%). This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 100 of the GLRA1 protein (p.Arg100His). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at