ClinVar Genomic variation as it relates to human health

Variant summary: The ASPA c.914C>A (p.Ala305Glu) variant involves the alteration of a conserved nucleotide and 4/4 in silico tools (SNPs&GO not captured due to low reliability index) predict a damaging outcome for this variant. These predictions are supported by a functional study, Kaul_1994, that indicates the variant eliminates ASPA enzyme activity in COS1 transfected cells. The variant of interest was observed in the large, broad control population, ExAC, with an allele frequency of 27/117066 (1/4336), which does not exceed the estimated maximal expected allele frequency for a pathogenic ASPA variant of 1/126. The variant of interest has been reported in multiple affected individuals, both homozygotes and compound heterozygotes. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

This established pathogenic variant has been previously reported as a homozygous and compound heterozygous change in patients with Canavan Disease (PMID: 20301412, 8023850, 10909858). Experimental studies have shown that this variant causes loss of ASPA enzyme activity (PMID: 22750302, 8023850). This variant is present in the heterozygous state in the gnomAD population database at a frequency of 0.02% (57/282352) and thus is presumed to be rare. It affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. Based on the available evidence, the c.914C>A (p.Ala305Glu) variant is classified as pathogenic.

NM_000049.2(ASPA):c.914C>A(A305E) is classified as pathogenic in the context of Canavan disease and can be associated with a severe or mild form of the disease. Sources cited for classification include the following: PMID 22850825, 22750302, 8023850 and 7668285. Classification of NM_000049.2(ASPA):c.914C>A(A305E) is based on the following criteria: This is a well-established pathogenic variant in the literature that has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

ACMG categories: PS3,PM1,PM2,PP3,PP4,PP5

The ASPA c.914C>A (p.Ala305Glu) variant is frequently reported in non-Jewish individuals with Canavan disease (CD). Across a selection of the available literature, the p.Ala305Glu variant has been identified in a homozygous state in eight patients with severe CD, in a compound heterozygous state in five patients with mild to classic CD, and in a heterozygous state in 13 patients in whom a second variant was not identified (Kaul et al. 1994; Shaag et al. 2005; Yalcinkaya et al. 2005; Janson et al. 2006; Sarret et al. 2015; Merrill et al. 2016). Control data are unavailable for this variant, which is reported at a frequency of 0.000372 in the European (non-Finnish) population of the Genome Aggregation Database. Cultured fibroblasts from affected individuals demonstrated negligible (0-5%) ASPA enzymatic activity as compared to fibroblasts from healthy controls (Yalcinkaya et al. 2005; Janson et al. 2006). Significantly reduced ASPA activity was also confirmed in various cell lines (Kaul et al. 1994; Janson et al. 2006; Sommer et al. 2012; Zano et al. 2013). Based on the collective evidence, the p.Ala305Glu variant is classified as pathogenic for Canavan disease. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

Functional analysis found that A305E is associated with significantly reduced enzyme activity compared to wild type (Sommer et al., 2012; Zano et al., 2013); This variant is associated with the following publications: (PMID: 25497124, 30834272, 16217711, 16437572, 28101991, 27927234, 7668285, 22850825, 8023850, 26586007, 21228398, 23233226, 22750302)

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

This sequence change replaces alanine, which is neutral and non-polar, with glutamic acid, which is acidic and polar, at codon 305 of the ASPA protein (p.Ala305Glu). This variant is present in population databases (rs28940574, gnomAD 0.04%). This missense change has been observed in individual(s) with Canavan disease (PMID: 8023850, 10909858, 16217711, 22850825). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 2607). 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: 8023850, 22750302). For these reasons, this variant has been classified as Pathogenic.

The c.914C>A (p.A305E) alteration is located in exon 6 (coding exon 6) of the ASPA gene. This alteration results from a C to A substitution at nucleotide position 914, causing the alanine (A) at amino acid position 305 to be replaced by a glutamic acid (E). Based on data from the Genome Aggregation Database (gnomAD) database, the ASPA c.914C>A alteration was observed in 0.02% (57/282352) of total alleles studied, with a frequency of 0.04% (48/128892) in the European (non-Finnish) subpopulation. This alteration has been reported in the homozygous and compound heterozygous states in patients with Canavan disease and is a common mutation that accounts for up to 60% of mutations in non-Ashkenazi Jewish populations (Kaul, 1994; Shaag, 1995; Kaul, 1996). This amino acid position is well conserved in available vertebrate species. Multiple in vitro studies have demonstrated that this mutation results in loss of ASPA protein activity, displays loss of flexibility resulting in decreased binding affinity, and can affect the order in the β-sheet structure at the C-terminus of the ASPA protein (Kaul, 1994; Sommer, 2012; Sreevishnupriya, 2012; Zano, 2013). The p.A305E alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.

One pathogenic variant, p.Ala305Glu, accounts for 30%-60% of pathogenic variants in non-Ashkenazi Jewish populations and approximately 1% of pathogenic variants in the Ashkenazi Jewish population.