ClinVar Genomic variation as it relates to human health

Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic (ClinVar ID: VCV000014716.9, PMID:20847235, PS1). It is observed at an low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.0000318). The variant was observed as assumed (i.e. paternity and maternity not confirmed) de novoo (3billion dataset, PM6). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.891, 3Cnet: 0.833, PP3). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

This mutation has been previously reported as disease-causing and was found once in our laboratory de novo and mosaic in a 2-year-old male with motor delays, absent speech, hypertonia, epilepsy, short statures, failure to thrive, vision loss, MRI suggestive of Leigh disease

Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene and are associated with D-2-hydroxyglutaric aciduria 2 (MIM#613657). Mutant IDH2 was unable to carry out the decarboxylation of isocitrate to a-ketoglutarate (a-KG), but instead gained the neomorphic activity to reduce a-KG to R(-)-2-hydroxyglutarete (2-HG) (PMID: 21647154). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0200 - Variant is predicted to result in a missense amino acid change from arginine to glutamine. (I) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v3) <0.001 for a dominant condition (10 heterozygotes, 0 homozygotes). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools and highly conserved with a minor amino acid change. (SP) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants. This variant is also located in the substrate binding region (Decipher, UniProt). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported in at least ten individuals with D-2-hydroxyglutaric aciduria 2 (ClinVar, PMID: 20847235). However, it should also be noted that the same variant has been reported in somatic tissues across various malignancies (PMIDs: 24589777, 21647154, 23949315). (SP) 1001 - This variant has strong functional evidence supporting abnormal protein function. Patient lymphoblast cell lines heterozygous for the p.(Arg140Gln) variant demonstrated increased conversion of 2-ketoglutarate to D-2-hydroxyglutarate compared with cells from healthy individuals (PMID: 21889589). (SP) 1203 - This variant has been shown to be de novo in the proband (parental status confirmed) (by trio analysis). However, it should be noted that mosaicism has been reported for this variant (PMID: 24049096). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

An enzyme assay which determines IDH2 activity in lymphoblast extracts confirmed that R140Q results in gain of function in D-2 hydroxyglutaric aciduria type 2 (Kranendijk et al., 2011); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 20171147, 34641967, 21889589, 20847235, 24049096, 23558173)

The c.419G>A (p.R140Q) alteration is located in exon 4 (coding exon 4) of the IDH2 gene. This alteration results from a G to A substitution at nucleotide position 419, causing the arginine (R) at amino acid position 140 to be replaced by a glutamine (Q). Based on data from gnomAD, the A allele has an overall frequency of 0.003% (9/282846) total alleles studied. The highest observed frequency was 0.010% (2/19944) of East Asian alleles. This alteration has been detected in multiple individuals with D-2-hydroxyglutaric aciduria type 2, including multiple cases of reported de novo occurrence. Additionally, somatic mosaicism for this alteration has been reported in an affected individual as well as an unaffected individual (Kranendijk, 2010; Nota, 2013). Another alteration at the same codon, c.418C>G (p.R140G), has been detected in an individual with D-2-hydroxyglutaric aciduria type 2 (Kranendijk, 2010). This amino acid position is highly conserved in available vertebrate species. An enzyme assay demonstrated that the mean reaction rate in D-2-HGA type II lymphoblasts with this alteration was 8-fold higher than that of controls and D2-HGA type I cells, with a corresponding 140-fold increase in intracellular D-2-hydroxyglutarate (D-2-HG) level (Kranendijk, 2011). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.

This variant has been reported to affect IDH2 protein function (PMID: 25398939). This sequence change replaces arginine with glutamine at codon 140 of the IDH2 protein (p.Arg140Gln). The arginine residue is highly conserved and there is a small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs121913502, ExAC 0.03%), and has an allele count higher than expected for a pathogenic variant (PMID: 28166811). This variant has been observed in individual(s) with D-2-hydroxyglutaric aciduria (PMID: 20847235). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 14716). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. For these reasons, this variant has been classified as Pathogenic.

DNA sequence analysis of the IDH2 gene demonstrated a sequence change, c.419G>A, in exon 4 that results in an amino acid change, p.Arg140Gln. This variant has been described in the EXAC database with a low population frequency of 0.01% (dbSNP rs121913502). The p.Arg140Gln change affects a highly conserved amino acid residue located in a domain of the IDH2 protein that is known to be functional. This pathogenic sequence change has previously been described in at least 14 patients with IDH2-related D2-hydroxyglutaric aciduira type II, including in the confirmed de novo state in some families (Kranendijk et al., 2010). In one family with the p.Arg140Gln pathogenic sequence change, the patient's mother was identified as having somatic mosaicism for the variant (Kranendijk et al., 2010). In vitro enzyme assays in lymphoblasts demonstrate that this variant has increased reaction rates compare to controls, and results in a gain of function (Kranendijk et. al., 2011)