ClinVar Genomic variation as it relates to human health

The c.1097G>A (p.Arg366His) variant in ACADVL has been reported in the literature in patients with VLCADD or increased C14:1 acylcarnitine levels (PP4; PMID: 9973285, 20060901, 27246109, 24263034, 32558070). The variant has been detected as homozygote (PMID:24263034), or compound heterozygote with truncating/pathogenic variants, however without phase confirmation (PMID: 32558070, 27246109, 20060901, PM3). The highest population minor allele frequency in gnomAD is 0.0001 in the South Asian population, which is lower than the ClinGen ACADVL Variant Curation Expert Panel threshold (<0.001) meeting this criterion (PM2_Supporting). This variant resides within a region defined as a mutational hotspot by the ClinGen ACADVL Variant Curation Expert Panel (PMID: 9973285, 20060901, PM1). The computational predictor REVEL gives a score of 0.98, which is above the threshold of 0.75, evidence that correlates with impact to ACADVL function (PP3). The ACADVL Variant Curation Expert Panel VCEP classified the variant as likely pathogenic based on (PP4, PM1, PM3, PM2_Supporting, PP3).

Not observed at a significant frequency in large population cohorts (gnomAD); 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: 16488171, 26385305, 20060901, 24263034, 27246109, 25456746, 28755359, 28871440, 31589614, 32558070, 32528171, 9973285)

The ACADVL c.1097G>A (p.Arg366His) missense variant has been reported in at least four studies in which it is identified in at least seven individuals with VLCAD deficiency including in a homozygous state in one individual, in a compound heterozygous state in three individuals, in cis with another missense variant, both of which are in trans with a third missense variant in one individual, and in a heterozygous state in two individuals in whom it is unclear if they carry a second variant (Andresen et al. 1999; Boneh et al. 2006; Antunes et al. 2013; Evans et al. 2016). The p.Arg366His variant was absent from 100 control alleles and is reported at a frequency of 0.000098 in the South Asian population of the Genome Aggregation Database. Biochemical studies confirmed the VLCAD deficiency in all patients. Western blot analysis revealed reduced or barely detectable protein levels in fibroblasts from a patient carrying the p.Arg366His variant (Andresen et al. 1999). Several studies note that the variant is associated with a milder phenotype (Gobin-Limballe et al. 2010; Antunes et al. 2013; Brown et al. 2014). Structural analysis of the VLCAD protein suggests that the p.Arg366His variant would induce major structural alterations in substrate-binding, FAD-binding and in enzyme monomer-monomer interactions (Gobin-Limballe et al. 2010). The Arg366 site is thought to be a potential hotspot for variants (Andresen et al. 1999). Based on the collective evidence, the p.Arg366His variant is classified as pathogenic for VLCAD deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

The NM_000018.3:c.1097G>A (NP_000009.1:p.Arg366His) [GRCH38: NC_000017.11:g.7223152G>A] variant in ACADVL gene is interpretated to be Pathogenic based on ACMG guidelines (PMID: 25741868). This variant has been reported in PMID: 9973285. This variant meets the following evidence codes reported in the ACMG guidelines: PS1, PS3

This variant has been observed as homozygous or compound heterozygous change in several individuals affected with very long chain acyl-CoA dehydrogenase (VLCAD)(PMID: 9973285, 20060901, 24263034, 27246109). This variant is also known as p.Arg326His in the literature. ClinVar contains an entry for this variant (Variation ID: 203580). A different amino acid change at the same residue (p.Arg366Cys) have been reported in association with VLCAD deficiency (PMID 8845838, 21932095) supporting the functional importance of this region of the protein. It is present in the heterozygous state in the gnomAD population database at a frequency of 0.003% (8/282884) and thus is presumed to be rare. The c.1166G>A (p.Arg389His) variant 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.1166G>A (p.Arg389His) variant is classified as Pathogenic.

The ACADVL c.1097G>A; p.Arg366His variant (rs112406105), also known as Arg326His, has been reported in individuals with VLCAD deficiency both in the homozygous state and as compound heterozygous with another ACADVL pathogenic variant (Andresen 1999, Antunes 2013, Evans 2016, Gobin-Limballe 2010). Additionally, a different alteration at this codon (p.Arg366Cys) has also been associated with VLCAD deficiency and is considered pathogenic (Andresen 1996, Hoffman 2012, Spiekerkoetter 2010). The p.Arg366His variant is listed in ClinVar (Variation ID: 203580) and observed in the general population with low overall allele frequency of 0.003% (8/282,884 alleles) in the Genome Aggregation Database. The arginine at codon 366 is highly conserved and computational analyses predict that this variant is deleterious (REVEL: 0.975). Based on the above information, the p.Arg366His variant is considered pathogenic. References: Andresen BS et al. Clear correlation of genotype with disease phenotype in very-long-chain acyl-CoA dehydrogenase deficiency. Am J Hum Genet. 1999 Feb;64(2):479-94. PMID: 9973285. Andresen BS et al. Cloning and characterization of human very-long-chain acyl-CoA dehydrogenase cDNA, chromosomal assignment of the gene and identification in four patients of nine different mutations within the VLCAD gene. Hum Mol Genet. 1996 Apr;5(4):461-72. PMID: 8845838. Antunes AP et al. Intermittent rhabdomyolysis with adult onset associated with a mutation in the ACADVL gene. J Clin Neuromuscul Dis. 2013 Dec;15(2):69-72. PMID: 24263034. Evans M et al. VLCAD deficiency: Follow-up and outcome of patients diagnosed through newborn screening in Victoria. Mol Genet Metab. 2016 Aug;118(4):282-7. PMID: 27246109. Gobin-Limballe S et al. Compared effects of missense mutations in Very-Long-Chain Acyl-CoA Dehydrogenase deficiency: Combined analysis by structural, functional and pharmacological approaches. Biochim Biophys Acta. 2010 May;1802(5):478-84. PMID: 20060901. Hoffman L et al. VLCAD enzyme activity determinations in newborns identified by screening: a valuable tool for risk assessment. J Inherit Metab Dis. 2012 Mar;35(2):269-77. PMID: 21932095. Spiekerkoetter U et al. Tandem mass spectrometry screening for very long-chain acyl-CoA dehydrogenase deficiency: the value of second-tier enzyme testing. J Pediatr. 2010 Oct;157(4):668-73. PMID: 20547398.

This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 366 of the ACADVL protein (p.Arg366His). This variant is present in population databases (rs112406105, gnomAD 0.01%). This missense change has been observed in individual(s) with very long chain acyl-CoA dehydrogenase (VLCAD) deficiency (PMID: 20060901, 24263034, 27246109). This variant is also known as p.Arg326His. ClinVar contains an entry for this variant (Variation ID: 203580). 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 ACADVL protein function with a positive predictive value of 95%. This variant disrupts the p.Arg366 amino acid residue in ACADVL. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 8845838, 9973285, 21932095; Invitae). 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.