ClinVar Genomic variation as it relates to human health

The Q326H (c.978 G>C) variant has been published in association with argininosuccinic aciduria (Balmer et al. 2014). The Q326H (c.978 G>C) variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The Q326H variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts the Q326H variant is probably damaging to the protein structure/function. A missense variant at the same residue (Q326L) has also been reported in association with argininosuccinic aciduria (Balmer et al. 2014), supporting the functional importance of this position of the protein. Furthermore, several in-silico splice prediction models predict that the c.978 G>C nucleotide substitution, resulting in Q326H, creates a cryptic donor site which may supplant the natural donor/acceptor site and lead to abnormal gene splicing. However, in the absence of RNA/functional studies, the actual effect of c.978 G>C on splicing in this individual is unknown. In summary, we interpret Q326H (c.978 G>C) as likely pathogenic.

Variant summary: ASL c.978G>C (p.Gln326His) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant impacts the last nucleotide of the exon, and therefore may impact splicing. Several computational tools predict a significant impact on normal splicing: Two predict the variant abolishes a 5' splicing donor site. Two predict the variant weakens a 5' donor site. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 1.3e-05 in 229934 control chromosomes. c.978G>C has been reported in the literature in individuals affected with Argininosuccinic Aciduria (Bamer_2014, Bijarnia-Mahay_2018). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.

The missense variant p.Q326H in ASL (NM_000048.4) has been previously reported in individuals affected with Argininosuccinic aciduria (Balmer C et al, 2014). The p.Q326H variant has a gnomAD frequency of 0.001305 % and is novel (not in any individuals) in 1000 Genomes. The amino acid Gln at position 326 is changed to a His changing protein sequence and it might alter its composition and physico-chemical properties. The p.Q326H missense variant is predicted to be damaging by both SIFT and PolyPhen2. The glutamine residue at codon 326 of ASL is conserved in all mammalian species. The nucleotide c.978 in ASL is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Likely Pathogenic. The observed variant was also detected in the spouse.

This sequence change affects codon 326 of the ASL mRNA. It is a 'silent' change, meaning that it does not change the encoded amino acid sequence of the ASL protein. This variant also falls at the last nucleotide of exon 13, which is part of the consensus splice site for this exon. This variant is present in population databases (rs764356037, gnomAD 0.007%). This variant has been observed in individual(s) with argininosuccinate lyase deficiency (PMID: 24166829, 30285816). ClinVar contains an entry for this variant (Variation ID: 426324). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. This variant disrupts the p.Gln326 amino acid residue in ASL. Other variant(s) that disrupt this residue have been observed in individuals with ASL-related conditions (PMID: 24166829), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic.