ClinVar Genomic variation as it relates to human health

Variant summary: The ACADM c.799G>A (p.Gly267Arg) variant involves the alteration of a conserved nucleotide. 5/5 in silico tools predict a damaging outcome for this variant, which was confirmed by at least one functional study (Sturm_2012). This variant was found in 26/121212 control chromosomes at a frequency of 0.0002145, which does not exceed the estimated maximal expected allele frequency of a pathogenic ACADM variant (0.0054233). The variant has been reported in numerous affected individuals in the literature in both the homozygous and compound heterozygous state (Andresen_2012, Sturm_2012, Gramer_2015). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

NM_000016.4(ACADM):c.799G>A(G267R) is classified as pathogenic in the context of medium chain acyl-CoA dehydrogenase deficiency. Sources cited for classification include the following: PMID: 20036593, 20434380, 23798014, 1684086, 24966162, 9158144 and 22542437. Classification of NM_000016.4(ACADM):c.799G>A(G267R) 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.‚Äã

The ACADM c.799G>A; p.Gly267Arg variant (rs121434274) is reported in the literature in the compound heterozygous or homozygous state in several individuals affected with medium-chain acyl-CoA dehydrogenase deficiency (Andresen 1997, Koster 2014, Maier 2005, Sturm 2012, Yokota 1991, Zschocke 2001). This variant is reported in ClinVar (Variation ID: 3588), and is found in the general population with an overall allele frequency of 0.020% (57/282726 alleles) in the Genome Aggregation Database. The glycine at codon 267 is highly conserved, and computational analyses (SIFT, PolyPhen-2) predict that this variant is deleterious. Functional analyses of the variant protein show a significant reduction in enzymatic activity (Andresen 1997, Zschocke 2001). Based on available information, this variant is considered to be pathogenic. References: Andresen BS et al. The molecular basis of medium-chain acyl-CoA dehydrogenase (MCAD) deficiency in compound heterozygous patients: is there correlation between genotype and phenotype? Hum Mol Genet. 1997 May;6(5):695-707. Koster KL et al. Functional studies of 18 heterologously expressed medium-chain acyl-CoA dehydrogenase (MCAD) variants. J Inherit Metab Dis. 2014 Nov;37(6):917-28. Maier EM et al. Population spectrum of ACADM genotypes correlated to biochemical phenotypes in newborn screening for medium-chain acyl-CoA dehydrogenase deficiency. Hum Mutat. 2005 May;25(5):443-52. Sturm M et al. Functional effects of different medium-chain acyl-CoA dehydrogenase genotypes and identification of asymptomatic variants. PLoS One. 2012;7(9):e45110. Yokota I et al. Molecular survey of a prevalent mutation, 985A-to-G transition, and identification of five infrequent mutations in the medium-chain Acyl-CoA dehydrogenase (MCAD) gene in 55 patients with MCAD deficiency. Am J Hum Genet. 1991 Dec;49(6):1280-91. Zschocke J et al. Molecular and functional characterisation of mild MCAD deficiency. Hum Genet. 2001 May;108(5):404-8.

The variant has been reported to be in trans with a pathogenic variant as either compound heterozygous or homozygous in at least 2 similarly affected unrelated individuals (PMID:1684086, 23028790, 16291504, 1684086, 22848008, 24966162, PM3_S). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PMID: 24966162, 9158144, PS3_S). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.000202, PM2_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.983, 3CNET: 0.998, PP3_P). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

The ACADM c.799G>A variant is predicted to result in the amino acid substitution p.Gly267Arg. This variant, which has also been referred to in the literature as p.Gly242Arg, has been documented in the homozygous or compound heterozygous state in multiple medium chain acyl-CoA dehydrogenase deficiency (MCADD) patients (Yokota et al. 1991. PubMed ID: 1684086; Sturm et al. 2012. PubMed ID: 23028790; Koster et al. 2014. PubMed ID: 24966162). In functional studies, the MCAD protein levels and enzyme activity were significantly reduced (Sturm et al. 2012. PubMed ID: 23028790; Koster et al. 2014. PubMed ID: 24966162). In summary, we classify this variant as pathogenic.

The p.Gly271Arg (NM_001127328.1 c.811G>A) variant in ACADM (also reported as NM_000016.4:p.Gly267Arg in the literature) has been reported in at least 4 homozygous and 5 compound heterozygous individuals with medium-chain acyl-coenzyme A dehydrogenase (MCAD) deficiency (Yokota 1991 PMID 1684086, Zschocke 2001 PMID: 11409868, Sturm 2012 PMID 23028790, Koster 2014 PMID 24966162). This variant has also been reported in ClinVar (Variation ID#3588) as pathogenic by multiple laboratories. It has been identified in 34/126698 of European chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs121434274), though this frequency is low enough to be consistent with a recessive carrier frequency. In vitro functional studies suggest that the p.Gly271Arg variant leads to reduced activity (Zschocke 2001 PMID: 11409868, Sturm 2012 PMID 23028790, Koster 2014 PMID 24966162). In summary, the p.Gly271Arg variant is pathogenic for MCAD deficiency in an autosomal recessive manner based upon observations in affected individuals and functional studies. ACMG/AMP Criteria applied: PS3, PM3,PP3,PP5.

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

The ACADM c.799G>A (p.Gly267Arg) missense variant has been reported in several studies in association with MCAD deficiency. Across a selection of available literature, the p.Gly267Arg variant has been found in at least 12 individuals affected with MCAD deficiency, in at least six in a compound heterozygous state, and in at least six in a homozygous state (Yokota et al. 1991; Zschocke et al. 2001; Maier et al. 2005; Sturm et al. 2012; Anderson et al. 2012). In general, the individuals who were homozygous for the variant were asymptomatic or presented with a mild phenotype, while individuals who were compound heterozygous for the variant displayed a moderate to severe phenotype (Maier et al. 2005; Sturm et al. 2012; Anderson et al. 2012). The p.Gly267Arg variant was found in two unaffected parents in a heterozygous state (Zschocke et al. 2001) and was absent from at least 12 controls. The p.Gly267Arg variant is reported at a frequency of 0.000487 in the South Asian population of the Genome Aggregation Database. The Gly267 residue is conserved. Expression studies of the p.Gly267Arg variant in E. coli revealed considerable residual MCAD activity of the protein (40%) compared to wild type (Andresen et al. 1997). In vitro activity of the p.Gly267Arg protein was markedly increased when co-expressed with GroESL chaperonins, indicating that the variant affects protein folding (Andresen et al. 1997). Another set of studies in E. coli showed that the p.Gly267Arg variant had low activity of <5% and was expressed at very low levels. This residue is predicted to be localized in a domain of beta-sheets involved in Flavin adenine nucleotide (FAD) binding (Koster et al. 2014). Based on the collective evidence, the p.Gly267Arg variant is classified as pathogenic for MCAD deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

The ACADM c.799G>A (p.G267R) variant has been previously reported as pathogenic. The variant has been found in the homozygous or compound heterozygous state in individuals with medium-chain acyl-coA dehydrogenase deficiency (PMID: 1684086; 11409868; 23028790).

Expression studies demonstrate a reduced (13% to less than 10%) residual MCAD enzyme activity compared to wild-type and reduced protein expression on western blot analysis (Koster et al., 2014; Sturm et al., 2012); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 23028790, 30609409, 31012112, 27760515, 20434380, 16291504, 25087612, 22975760, 24966162, 1684086, 9158144, 28492532, 23798014, 20036593, 25940036, 31589614, 32853555)

This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 267 of the ACADM protein (p.Gly267Arg). This variant is present in population databases (rs121434274, gnomAD 0.05%). This missense change has been observed in individual(s) with MCAD deficiency (PMID: 1684086, 16291504, 22848008, 23028790; Invitae). ClinVar contains an entry for this variant (Variation ID: 3588). 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 ACADM protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects ACADM function (PMID: 9158144, 24966162). For these reasons, this variant has been classified as Pathogenic.

Based on the classification scheme VCGS_Germline_v1.3.5, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with deficiency of medium chain acyl-CoA dehydrogenase (MCAD) (MIM#201450). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0115 - Variants in this gene are known to have variable expressivity. Clinical presentation varies from asymptomatic to fulminant course (OMIM). (I) 0200 - Variant is predicted to result in a missense amino acid change from glycine to arginine. (I) 0251 - This variant is heterozygous. (I) 0304 - Variant is present in gnomAD <0.01 (v4) for a recessive condition (338 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v4; 1 heterozygote, 0 homozygotes). (I) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0600 - Variant is located in the annotated Acyl-CoA dehydrogenase, C-terminal domain (DECIPHER). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported as likely pathogenic/pathogenic by multiple clinical laboratories in ClinVar. (SP) 1205 - This variant has been shown to be maternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign