ClinVar Genomic variation as it relates to human health

The p.R71H pathogenic mutation (also known as c.212G>A), located in coding exon 1 of the ASPA gene, results from a G to A substitution at nucleotide position 212. The arginine at codon 71 is replaced by histidine, an amino acid with highly similar properties. This alteration has been detected in trans with a pathogenic mutation (p.Y231*) in ASPA by our laboratory. This mutation was identified in conjunction with another known mutation p.A305E in two siblings who presented with mild form of Canavan disease; ASPA enzymatic activity was significantly low in fibroblasts from these siblings (Janson CG et al. Ann. Neurol., 2006 Feb;59:428-31). A homozygous p.R71H mutation was also reported in another patient with mild Canavan disease (Velinov M et al. Clin. Genet., 2008 Mar;73:288-9). Structural analysis revealed that the arginine residue likely stabilizes substrate binding and may guide NAA to the active site (Bitto E et al. Proc. Natl. Acad. Sci. U.S.A., 2007 Jan;104:456-61). In vitro studies showed that R71H mutant protein has reduced catalytic activity (Janson CG et al. Ann. Neurol., 2006 Feb;59:428-31; Zano S et al. J. Inherit. Metab. Dis., 2013 Jan;36:1-6). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation.

The ASPA c.212G>A (p.Arg71His) variant has been reported in three studies and is found in a total of three individuals with a mild form of Canavan disease including one individual in a homozygous state and two sisters in a compound heterozygous state (Janson et al. 2006; Velinov et al. 2007). Control data are unavailable for this variant, which is reported at a frequency of 0.00197 in the European (Finnish) population of the Exome Aggregation Consortium. Functional studies in individual fibroblasts showed only 0% to 5% of ASPA activity compared to wild type (Janson et al. 2006). Bitto et al. (2007) determined the crystal structure of APSA and showed that the Arg71 residue lies in the ASPA active site and proposed a role in substrate binding. Hershfield et al. (2007) used homology-based modeling to analyze the function of the p.Arg71His variant and also concluded that Arg71 was located in the active site and was involved in substrate binding. Expression studies in P. pastoris by Zano et al. (2013) showed that the variant enzyme had 11% of wild type activity and reduced stability. The Arg71 residue is highly conserved. Based on the evidence, the p.Arg71His variant is classified as likely pathogenic for Canavan disease. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 71 of the ASPA protein (p.Arg71His). This variant is present in population databases (rs104894553, gnomAD 0.2%). This missense change has been observed in individual(s) with Canavan disease (PMID: 16437572, 18070137, 25107638). 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: 2616). 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 ASPA protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects ASPA function (PMID: 16437572, 22850825). For these reasons, this variant has been classified as Pathogenic.

Published functional studies demonstrate loss of enzymatic activity (PMID: 16437572, 22850825); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 22850825, 17194761, 18070137, 16437572, 25668701, 34426522, 32975148, 25107638, 25003821)