chr15-90088703-G-C
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PM5PP3_ModeratePP5
The NM_002168.4(IDH2):c.418C>G(p.Arg140Gly) variant causes a missense change involving the alteration of a non-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. R140L) has been classified as Likely pathogenic.
Frequency
Consequence
NM_002168.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
IDH2 | NM_002168.4 | c.418C>G | p.Arg140Gly | missense_variant | 4/11 | ENST00000330062.8 | |
IDH2 | NM_001289910.1 | c.262C>G | p.Arg88Gly | missense_variant | 4/11 | ||
IDH2 | NM_001290114.2 | c.28C>G | p.Arg10Gly | missense_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
IDH2 | ENST00000330062.8 | c.418C>G | p.Arg140Gly | missense_variant | 4/11 | 1 | NM_002168.4 | P1 | |
IDH2 | ENST00000540499.2 | c.262C>G | p.Arg88Gly | missense_variant | 4/11 | 2 | |||
IDH2 | ENST00000559482.5 | c.208-201C>G | intron_variant | 5 | |||||
IDH2 | ENST00000560061.1 | c.*43C>G | 3_prime_UTR_variant, NMD_transcript_variant | 2/9 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome Cov.: 33
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
D-2-hydroxyglutaric aciduria 2 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 01, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at