chr5-151829060-T-G
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP3_StrongPP5
The NM_000171.4(GLRA1):c.920A>C(p.Tyr307Ser) 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y307C) 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 11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GLRA1 | NM_000171.4 | c.920A>C | p.Tyr307Ser | missense_variant | 8/9 | ENST00000274576.9 | |
GLRA1 | NM_001146040.2 | c.920A>C | p.Tyr307Ser | missense_variant | 8/9 | ||
GLRA1 | NM_001292000.2 | c.671A>C | p.Tyr224Ser | missense_variant | 7/8 | ||
GLRA1 | XM_047417105.1 | c.968A>C | p.Tyr323Ser | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GLRA1 | ENST00000274576.9 | c.920A>C | p.Tyr307Ser | missense_variant | 8/9 | 1 | NM_000171.4 | P4 | |
GLRA1 | ENST00000455880.2 | c.920A>C | p.Tyr307Ser | missense_variant | 8/9 | 1 | A1 | ||
GLRA1 | ENST00000462581.6 | c.*678A>C | 3_prime_UTR_variant, NMD_transcript_variant | 7/8 | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 31
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Hyperekplexia 1 Pathogenic:1
Pathogenic, no assertion criteria provided | curation | GeneReviews | Oct 04, 2012 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at