ClinVar Genomic variation as it relates to human health

NM_000159.2(GCDH):c.1204C>T(R402W) is classified as likely pathogenic in the context of GCDH-related glutaric acidemia. Sources cited for classification include the following: PMID 8900227, 10699052, 24973495 and 18775954. Classification of NM_000159.2(GCDH):c.1204C>T(R402W) is based on the following criteria: This variant has been observed more frequently in patients with clinical diagnoses than in healthy populations and there is functional data showing deficient protein function. Please note: this variant was assessed in the context of healthy population screening.

The c.1204C>T (p.R402W) alteration is located in exon 11 (coding exon 10) of the GCDH gene. This alteration results from a C to T substitution at nucleotide position 1204, causing the arginine (R) at amino acid position 402 to be replaced by a tryptophan (W). Based on data from gnomAD, the T allele has an overall frequency of 0.03% (89/282634) total alleles studied. The highest observed frequency was 0.08% (19/25112) of European (Finnish) alleles. This mutation has been reported in the homozygous and compound heterozygous state in multiple individuals with GCDH-related glutaricadicuria (Biery, 1996; Busquets, 2000; Zayed, 2019; Pokora, 2019). In E. coli and BHK cells, GCDH activity was reduced compared to wild type (Biery, 1996; Keyser, 2008). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.

Variant summary: The GCDH c.1204C>T (p.Arg402Trp) variant involves the alteration of a conserved nucleotide. 4/4 in silico tools predict a damaging outcome for this variant (SNPs&GO not captured due to low reliability index). This variant was found in 27/120918 control chromosomes at a frequency of 0.0002233, which does not exceed the estimated maximal expected allele frequency of a pathogenic GCDH variant (0.0035355). The variant was found in multiple affected individuals with an established diagnosis of GA-I based on the clinical symptoms, characteristic findings on neuroimaging and quantitative analysis of organic acids in urine. Busquets (2000) and Zschocke (2000) report the frequency of the variant of interest in affected individuals as 22% and 25%, respectively. Functional studies using expression systems show the variant to have a complete loss of GCDH activity (Biery_1996, Keyser_2008). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

The GCDH c.1204C>T (p.Arg402Trp) variant has been described in at least nine studies and is found in at least 63 individuals with glutaric acidemia, including 26 in a homozygous state, 18 in a compound heterozygous state, and nine in a heterozygous state (Biery et al. 1996; Schwartz et al. 1998; Busquets et al. 2000a; Busquets et al. 2000b; Busquets et al. 2000c; Zschocke et al. 2000; Fraidakis et al. 2014; Georgiou et al. 2014; Gupta et al. 2015). The variant is found in an additional 24 disease alleles of unknown zygosity (Biery et al. 1996; Zschocke et al. 2000). The p.Arg402Trp variant has been described as the most common variant in different populations being present in 10-20% of alleles in affected individuals (Zschocke et al. 2000; Fraidakis et al. 2014). The p.Arg402Trp variant was absent from 100 unrelated Spanish controls and is reported at a frequency of 0.00076 in the European (Finnish) population of the Exome Aggregation Consortium. Expression of the p.Arg402Trp variant in E.coli and cultured fibroblasts showed reduced GCD activity compared to wild type, with 3% and <1% residual activity, respectively (Biery et al. 1996; Busquets et al. 2000b; Schwartz et al. 1998). Keyser et al. (2008) also demonstrated a reduced enzyme activity for the variant of 1.6% of wild type in mammalian cells and an increased degradation of the protein compared to wild type. The Arg402 residue is highly conserved. Based on the collective evidence, the p.Arg402Trp variant is classified as pathogenic for glutaric acidemia. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

PS3, PS4_Supporting, PM2, PM3_Strong, PP4

Functional studies in E.coli and BHK cells transfected with R402W mutant plamids demonstrated reduced GCDH enzyme expression as compared to wild type, and upon cross-linkage, the formation of homotetrameric GCDH was strongly impaired in the R402W mutants (Biery et al., 1996; Keyser et al., 2008); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 9711871, 32056211, 10699052, 25087612, 8900227, 18775954, 10960496, 24973495, 25762492, 28438223, 28352331, 29292490, 30217722, 30570710, 31062211, 25256449, 10649503, 20732827, 31589614, 32777384, 32240488)

The missense c.1204C>T(p.Arg402Trp) variant in GCDH gene has been reported previously in homozygous and compound heterozygous state in individuals affected with type I glutaric aciduria (Boy et al. 2017; Zayed et al. 2019). The variant is the most common missense change in individuals affected with type I glutaric aciduria (Zayed et al. 2019). Experimental studies show that this variant leads to rapid intramitochondrial degradation causing a significantly reduced protein compared with cells expressing wild-type protein (Keyser et al. 2008). The p.Arg402Trp variant is reported with an allele frequency of 0.03% in the gnomAD exomes database and is novel (not in any individuals) in 1000 Genomes database. This variant has been reported to the ClinVar database as Likely Pathogenic / Pathogenic (multiple submissions). The amino acid change p.Arg402Trp in GCDH is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Arg at position 402 is changed to a Trp changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Pathogenic.

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 402 of the GCDH protein (p.Arg402Trp). This variant is present in population databases (rs121434369, gnomAD 0.07%). This missense change has been observed in individual(s) with glutaric acidemia I and is the most common cause of glutaric acidemia I in Europe (PMID: 8900227, 10649503, 11073722, 20732827, 28352331, 28438223). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 2085). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt GCDH protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects GCDH function (PMID: 8900227, 18775954). For these reasons, this variant has been classified as Pathogenic.

GCDH: PM3:Very Strong, PS3, PM1, PM2, PM5, PP3

Most common pan ethnic pathogenic variant