ClinVar Genomic variation as it relates to human health

Variant summary: ACSF3 c.1672C>T (p.Arg558Trp) results in a non-conservative amino acid change located in the C-terminal domain (IPR025110) of 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 0.0026 in 248458 control chromosomes (gnomAD). The variant, c.1672C>T, has been reported in the literature in multiple homozygous and compound heterozygous individuals affected with Combined Malonic and Methylmalonic Aciduria (e.g. Sloan_2011, Pupavac_2016, Levtova_2019). These data indicate that the variant is very likely to be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Five 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 pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

PM1, PS3, PM3

The p.Arg558Trp variant in the ACSF3 gene has been identified in the homozygous or compound heterozygous state in many individuals diagnosed with CMAMMA (Sloan et al., 2011; Pupavac et al., 2016; Levtova et al., 2019). In several cases, this variant was confirmed to be in trans with another likely pathogenic or pathogenic variant (p.E359K, 1.7 Mb deletion spanning ACSF3), consistent with autosomal recessive inheritance. The p.Arg558Trp variant has been identified in 612/127,754 European non-Finnish chromosomes, including 1 homozygote, by the Genome Aggregation Database (http://gnomad.broadinstitute.org/). Although this variant has been seen in the general population, its frequency is low enough to be consistent with an autosomal recessive condition with reduced penetrance. Functional studies of the p.Arg558Trp variant are supportive of a deleterious effect to the protein showing significantly increased accumulation of methylmalonic acid in patient fibroblasts (Sloan et al., 2011). Computational tools also predict that this variant is deleterious; however, the accuracy of in silico algorithms is limited. These data were assessed using the ACMG/AMP variant interpretation guidelines. In summary, there is sufficient evidence to classify the p.Arg558Trp variant as pathogenic for autosomal recessive combined malonic and methylmalonic aciduria based on the information above. [ACMG evidence codes used: PM3_VeryStrong; PS3_Supporting; PP3]

This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 558 of the ACSF3 protein (p.Arg558Trp). This variant is present in population databases (rs141090143, gnomAD 0.5%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with methylmalonic acidemia (PMID: 21841779, 26827111; Invitae). 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: 31134). 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 ACSF3 protein function with a positive predictive value of 95%. For these reasons, this variant has been classified as Pathogenic.

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: 30609409, 21841779, 31376476, 26827111, 28468868, 29555771, 29858964, 30041674, 30740739, 30665703, 30487145, 31462756, 31980526, 34426522, 34440436, 33625768, 33726816, 34662886, 33879512, 36717752, 17762044, 38536866)

PP4, PM3, PS3, PS4

The p.Arg558Trp variant in ACSF3 has been reported in >10 homozygous or compound heterozygous individuals with features of combined malonic and methylmalonic acidemia, however some of those patients were asymptomatic and only had elevated methyl malonic acid levels. In several cases, this variant was found with another likely pathogenic or pathogenic variant in ACSF3, and confirmed to be in trans in at least 1 individual (Sloan 2011 PMID: 21841779, Pupavac 2016 PMID: 26827111, Levtova 2019 PMID: 30740739). At least one patient responded to cobalamin treatment (Pupavac 2016 PMID: 26827111). It was found to segregate in one sibling who had elevated methyl malonic acid levels but without clinical concerns (Levtova 2019 PMID: 30740739). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 31134). In addition, this variant has been identified in 0.58% (6822/1179774) of European chromosomes, including 18 total homozygotes by gnomAD (http://gnomad.broadinstitute.org, v.4.0.0). Although the frequency is appreciable, it is consistent with the clinical manifestation of the disease. In vitro functional studies using fibroblasts from affected homozygous and compound heterozygous individuals show increased accumulation of methylmalonic acid fibroblasts, that was restored to normal levels after transfection of a viral vector containing the ACSF3 gene, (Sloan 2011 PMID: 21841779). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal recessive combined malonic and methylmalonic acidemia, however the impact of the biochemical phenotype on clinical features is variable. ACMG/AMP Criteria applied: PM3_VeryStrong, PP4, PP1.

ACSF3: PM3:Very Strong, PM2

The ACSF3 c.1672C>T variant is predicted to result in the amino acid substitution p.Arg558Trp. This variant has been reported in both the compound heterozygous and homozygous states in multiple unrelated individuals diagnosed with combined malonic and methylmalonic aciduria (CMAMMA; Sloan et al. 2011. PubMed ID: 21841779; Pupavac et al. 2016. PubMed ID: 26827111) and has been found to be one of the most commonly reported pathogenic variants in ACSF3 (Levtova et al. 2019. PubMed ID: 30740739).This variant is reported in 0.48% of alleles in individuals of European (Non-Finnish) descent in gnomAD. This variant is interpreted as pathogenic.