ClinVar Genomic variation as it relates to human health

NM_000049.2(ASPA):c.503G>A(R168H) is a missense variant classified as likely pathogenic in the context of Canavan disease. R168H has been observed in cases with relevant disease (PMID: 10909858, 23971085, 28101991). Functional assessments of this variant are available in the literature (PMID: 22750302). Internal structural analysis of the variant is supportive of pathogenicity. R168H has been observed in population frequency databases (gnomAD: NFE 0.01%). In summary, NM_000049.2(ASPA):c.503G>A(R168H) is a missense variant that has internal structural support for pathogenicity and has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening.

Variant summary: ASPA c.503G>A (p.Arg168His) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 5.2e-05 in 251402 control chromosomes. This frequency is not higher than expected for a pathogenic variant in ASPA causing Canavan Disease (5.2e-05 vs 0.0079), allowing no conclusion about variant significance. c.503G>A has been reported in the literature in individuals affected with Canavan Disease in the homozygous and heterozygous state (Sistermans_2000, Mendes_2017). These data indicate that the variant is likely to be associated with disease. The variant has been reported to have loss of ASPA activity in transfected HEK293 cells (Sommer_2012) . Six clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic (n=2) and likely pathogenic (n=4). Based on the evidence outlined above, the variant was classified as pathogenic.

The missense variant p.R168H in ASPA (NM_000049.2) has been observed in several individuals affected with Canavan disease (E A Sistermans et al, 2000; Marisa I Mendes et al, 2017). This variant has been reported to affect ASPA protein function (A Sommer et al, 2012). This missense has been submitted to ClinVar as Pathogenic/Likely Pathogenic. The p.R168H variant is observed as heterozygous in 13 (0.005%) alleles from individuals of all background in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The p.R168H missense variant is predicted to be damaging by both SIFT and PolyPhen2. The nucleotide c.503 in ASPA is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Pathogenic.

A Homozygote Missense variant c.503G>A in Exon 3 of the ASPA gene that results in the amino acid substitution p.Arg168His was identified. The observed variant has a minor allele frequency of 0.00005% in gnomAD exomes and is novel in genomes. The severity of the impact of this variant on the protein is medium, based on the effect of the protein and REVEL score . Rare Exome Variant Ensemble Learner (REVEL) is an ensembl method for predicting the pathogenicity of missense variants based on a combination of scores from 13 individual tools: MutPred, FATHMM v2.3, VEST 3.0, PolyPhen-2, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP++, SiPhy, phyloP, and phastCons. The REVEL score for an individual missense variant can range from 0 to 1, with higher scores reflecting greater likelihood that the variant is disease-causing. ClinVar has also classified this variant as Pathogenic [Variant ID : 550697]. The observed variation has previously been reported for Canavan disease by Mendes, Marisa I., et al., 2017. Functional assessments proves the pathogenicity of the variant by Sommer, Anke, and Jörn Oliver Sass. , 2012. For these reasons this variant has been classified as Pathogenic.

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 168 of the ASPA protein (p.Arg168His). This variant is present in population databases (rs770706390, gnomAD 0.009%). This missense change has been observed in individuals with Canavan disease (PMID: 10909858, 21520333, 28101991). ClinVar contains an entry for this variant (Variation ID: 550697). 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: 22750302). This variant disrupts the p.Arg168 amino acid residue in ASPA. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8659549, 16854607). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.