chrX-14581319-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PS1_ModeratePM2PP3_StrongPP5
The NM_002063.4(GLRA2):āc.407A>Gā(p.Asn136Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000166 in 1,203,535 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another nucleotide change resulting in same amino acid change has been previously reported as Likely pathogenicin UniProt.
Frequency
Consequence
NM_002063.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GLRA2 | NM_002063.4 | c.407A>G | p.Asn136Ser | missense_variant | 4/9 | ENST00000218075.9 | NP_002054.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GLRA2 | ENST00000218075.9 | c.407A>G | p.Asn136Ser | missense_variant | 4/9 | 1 | NM_002063.4 | ENSP00000218075 | A1 | |
GLRA2 | ENST00000355020.9 | c.407A>G | p.Asn136Ser | missense_variant | 4/9 | 1 | ENSP00000347123 | P4 | ||
GLRA2 | ENST00000415367.2 | n.658A>G | non_coding_transcript_exon_variant | 4/9 | 3 | |||||
GLRA2 | ENST00000443437.6 | c.*334A>G | 3_prime_UTR_variant, NMD_transcript_variant | 6/11 | 2 | ENSP00000387756 |
Frequencies
GnomAD3 genomes AF: 0.00000896 AC: 1AN: 111649Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33831
GnomAD4 exome AF: 9.16e-7 AC: 1AN: 1091886Hom.: 0 Cov.: 29 AF XY: 0.00000280 AC XY: 1AN XY: 357464
GnomAD4 genome AF: 0.00000896 AC: 1AN: 111649Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33831
ClinVar
Submissions by phenotype
Intellectual developmental disorder, X-linked, syndromic, Pilorge type Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 26, 2022 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at