ClinVar Genomic variation as it relates to human health

The MCCC2 c.1015G>A (p.Val339Met) missense variant has been reported in at least four studies in which it was found in at least seven individuals with 3-Methylcrotonyl-CoA carboxylase (3-MCC) deficiency, including in two individuals in a compound heterozygous state and in five individuals in a heterozygous state without a second allele detected (Baumgartner et al. 2001; Wolfe et al. 2007; Grunert et al. 2012; Morscher et al. 2012). The p.Val339Met variant was also found in a compound heterozygous state in nine asymptomatic individuals, eight of whom were identified during newborn screening and presented with biochemical markers associated with 3-MCC deficiency (Grunert et al. 2012; Fonseca et al. 2016). In addition, the variant was also detected in a compound heterozygous state in one individual in whom affected status was unknown and in a heterozygous state in one asymptomatic individual (Grunert et al. 2012; Fonseca et al. 2016). Several of the asymptomatic compound heterozygous individuals carried null alleles on the second allele (Fonseca et al. 2016). The p.Val339Met variant was absent from 200 control chromosomes (Morscher et al. 2012) and is reported at a frequency of 0.00279 in the Other population of the Genome Aggregation Database. The Val339 residue is conserved across species and expression studies in proband fibroblasts found the p.Val339Met variant resulted in 4-12% residual enzyme activity compared to wild type (Baumgartner et al. 2001; Wolfe et al. 2007). Based on the collective evidence, the p.Val399Met variant is classified as likely pathogenic for 3-MCC deficiency. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

Same or different nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000203805, PMID:11181649). Functional studies provide strong evidence of the variant having a damaging effect on the gene or gene product (PS3_S, PMID:11181649). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.951>=0.6). It is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.0008286). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.

ACMG classification criteria: PS3, PM3, PP3

Variant summary: MCCC2 c.1015G>A (p.Val339Met) results in a 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 0.00078 in 251374 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in MCCC2 causing Methylcrotonyl-CoA Carboxylase Deficiency (0.00078 vs 0.0042), allowing no conclusion about variant significance. c.1015G>A has been reported in the literature in multiple individuals affected with Methylcrotonyl-CoA Carboxylase Deficiency. 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. The following publications have been ascertained in the context of this evaluation (PMID: 30510438, 22642865). Seventeen submitters have cited clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.

The c.1015G>A (p.V339M) alteration is located in exon 11 (coding exon 11) of the MCCC2 gene. This alteration results from a G to A substitution at nucleotide position 1015, causing the valine (V) at amino acid position 339 to be replaced by a methionine (M). This mutation has been reported in both the homozygous and compound heterozygous state in individuals with 3-methylcrotonyl-CoA carboxylase 2 deficiency (Grünert, 2012; Fonseca, 2016; Posey, 2017; Alsemari, 2018; Monies, 2019). Several were asymptomatic and identified via newborn screening; however, at least two individuals presented with developmental delay or failure to thrive (Fonseca, 2016; Monies, 2019). One patient with a more complex presentation of intellectual disability, short stature, osteopetrosis, calcification of basal ganglia, and thinning of the corpus callosum was homozygous for this mutation as well as variants in three other genes; MCCC2 p.V339M was not thought to explain the patient's phenotype (Alsemari, 2018). In vitro analysis of this mutation demonstrated reduced enzyme activity (4%) compared to wild type (Baumgartner, 2001). This alteration is predicted to be deleterious by in silico analysis. Based on the available evidence, this alteration is classified as pathogenic.

This variant was previously reported in several individuals affected with 3-methylcrotonyl-CoA carboxylase deficiency as compound heterozygous and as heterozygous [PMID: 22642865, 27601257, 11181649, 22642865, 22264772]. Functional studies have shown that the variant is associated with approximately 4% residual enzyme activity compared to wildtype in vitro [PMID: 11181649, 17908719].

Published functional studies demonstrated that V339M was associated with approximately 4% residual enzyme activity compared to wildtype (Baumgartner et al., 2001); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 25525159, 25087612, 27601257, 16835865, 27033733, 11181649, 27391121, 26990548, 27959697, 22642865, 25356967, 22264772, 17908719, 30510438, 31130284, 34426522, 33238263, 32778825, 33077954)

This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 339 of the MCCC2 protein (p.Val339Met). This variant is present in population databases (rs150591260, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with 3-methylcrotonyl-CoA carboxylase (3MCC) deficiency with low MCCC2 enzymatic activity (PMID: 11181649, 22264772, 22642865, 27601257). 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: 203805). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MCCC2 protein function. Experimental studies have shown that this missense change affects MCCC2 function (PMID: 11181649). For these reasons, this variant has been classified as Pathogenic.

Based on the classification scheme VCGS_Germline_v1.3.4, 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 3-Methylcrotonyl-CoA carboxylase 2 deficiency (MIM#210210). (I) 0106 - This gene is associated with autosomal recessive disease. (I) 0112 - The condition associated with this gene has incomplete penetrance (PMID: 27033733). (I) 0115 - Variants in this gene are known to have variable expressivity (PMID: 26566957). (I) 0200 - Variant is predicted to result in a missense amino acid change from valine to methione. (I) 0252 - This variant is homozygous. (I) 0304 - Variant is present in gnomAD (v2) <0.01 for a recessive condition (209 heterozygotes, 0 homozygotes). (SP) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (v2) (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 CoA carboxyltransferase C-terminal (UniProt). (I) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported multiple times as pathogenic in ClinVar. It has also been reported in both homozygous and compound heterozygous individuals with 3-Methylcrotonyl-CoA carboxylase 2 deficiency (PMID: 34899149, 35281663). (SP) 1209 - This variant has been shown to be both maternally and paternally inherited (biallelic) (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign

MCCC2: PM3:Strong, PM2, PP1, PP3, PP4, PS3:Supporting

The MCCC2 c.1015G>A variant is predicted to result in the amino acid substitution p.Val339Met. This variant has been reported in the compound heterozygous state in many patients biochemically and/or enzymatically diagnosed with 3-methylcrotonyl-CoA carboxylase deficiency (e.g., Grünert et al. 2012. PubMed ID: 22642865; Fonseca et al. 2016. PubMed ID: 27601257). This variant has been reported to greatly decrease the activity of the 3-methylcrotonyl-CoA carboxylase enzyme (Baumgartner et al. 2001. PubMed ID: 11181649). It is reported in 0.18% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. Based on the collective evidence, this variant is interpreted as pathogenic.