rs879254016
Variant summary
Our verdict is Pathogenic. Variant got 11 ACMG points: 11P and 0B. PM1PM2PM5PP2PP3_Strong
The NM_000834.5(GRIN2B):c.2453T>G(p.Met818Arg) 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. M818L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000834.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GRIN2B | NM_000834.5 | c.2453T>G | p.Met818Arg | missense_variant | Exon 13 of 14 | ENST00000609686.4 | NP_000825.2 | |
GRIN2B | NM_001413992.1 | c.2453T>G | p.Met818Arg | missense_variant | Exon 14 of 15 | NP_001400921.1 | ||
GRIN2B | XM_005253351.3 | c.239T>G | p.Met80Arg | missense_variant | Exon 3 of 4 | XP_005253408.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GRIN2B | ENST00000609686.4 | c.2453T>G | p.Met818Arg | missense_variant | Exon 13 of 14 | 1 | NM_000834.5 | ENSP00000477455.1 | ||
GRIN2B | ENST00000637214.1 | c.69+41433T>G | intron_variant | Intron 1 of 1 | 5 | ENSP00000489997.1 | ||||
GRIN2B | ENST00000628166.2 | n.713T>G | non_coding_transcript_exon_variant | Exon 5 of 5 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Intellectual disability, autosomal dominant 6;C4015316:Developmental and epileptic encephalopathy, 27 Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at