ClinVar Genomic variation as it relates to human health

The Arg91LysfsX14 variant in MMACHC has been identified in homozygosity in 81 individuals and in compound heterozygosity in 86 individuals with methylmalonic aciduria and homocystinuria, cblC type (Lerner-Ellis 2006, Richard 2009, Liu 2010). This frameshift variant is predicted to alter the protein’s amino acid sequence beginning at position 91 and lead to a premature termination codon 14 amino acids downstream. This alteration is then predicted to lead to a truncated or absent protein. In summary, this variant meets our criteria for pathogenicity.

Variant summary: The MMACHC c.271dupA (p.Arg91Lysfs) variant results in a premature termination codon, predicted to cause a truncated or absent MMACHC protein due to nonsense mediated decay, which are commonly known mechanisms for disease. This variant was found in 132/120196 control chromosomes at a frequency of 0.0010982, which does not exceed the estimated maximal expected allele frequency of a pathogenic MMACHC variant (0.0030542). The variant is a well known common disease variant and has been reported in numerous affected individuals in the literature, including individuals carrying the variant in the homozygous and compound heterozygous state (Lerner-Ellis_2006). Supporting the pathogenicity of this variant, incorporation of labelled methyltetrahydrofolate and propionate into cellular macromolecules was significantly affected in patients with homozygous or compound heterozygous c.271dupA (Lerner-Ellis_2006). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic.

NM_015506.2(MMACHC):c.271dupA(R91Kfs*14) is classified as pathogenic in the context of cblC type methylmalonic aciduria and homocystinuria and may be associated with the early onset form of disease. Sources cited for classification include the following: PMID 19370762. Classification of NM_015506.2(MMACHC):c.271dupA(R91Kfs*14) is based on the following criteria: The variant causes a premature termination codon that is expected to be targeted by nonsense-mediated mRNA decay and is reported in individuals with the relevant phenotype. Please note: this variant was assessed in the context of healthy population screening.

The c.271dupA (p.R91Kfs*14) alteration, located in exon 2 (coding exon 2) of the MMACHC gene, consists of a duplication of A at position 271, causing a translational frameshift with a predicted alternate stop codon after 14 amino acids. This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. Based on data from the Genome Aggregation Database (gnomAD), the MMACHC c.271dupA alteration was observed in 0.11% (314/280836) of total alleles studied, with a frequency of 0.28% (29/10356) in the Ashkenazi Jewish subpopulation. This mutation has been reported in the homozygous and compound heterozygous states in multiple unrelated patients with methylmalonic aciduria and homocystinuria, cblC type. It is the most frequently identified MMACHC mutation accounting for 30-50% of alleles and is typically associated with infantile onset disease (Lerner-Ellis, 2006; Richard, 2009; Fischer, 2014). Based on the available evidence, this alteration is classified as pathogenic.

The MMACHC c.271dupA (p.Arg91LysfsTer14) variant, also referred to as c.270_271insA, results in a frameshift variant and is predicted to result in premature termination of the protein. The p.Arg91LysfsTer14 variant is well described in the literature and is reported as the most common pathogenic variant in the MMACHC gene accounting for approximately 40% of disease alleles (Manoli et al. 2016). The variant has been reported in at least 12 studies in which it was found in over 270 individuals with disorders of intracellular cobalamin metabolism, including at least 127 in a homozygous state and 143 in a compound heterozygous state (Lerner-Ellis et al. 2006; Morel et al. 2006; Heil et al. 2007; Nogueira et al. 2008; Lerner-Ellis et al. 2009; Perez et al. 2010; Frattini et al. 2010; Tsai et al. 2011; Komhoff et al. 2103; Gizicki et al. 2014; Fischer et al. 2014; Collison et al. 2015). The variant was absent from 105 controls and is reported at a frequency of 0.00173 in the European American population of the Exome Sequencing Project. Individuals who carry the p.Arg91LysfsTer14 variant in a homozygous state tend to have an earlier age of onset of the condition while the age of onset of disease when carried in the compound heterozygous state varies depending on the second variant (Morel et al. 2006). Functional studies in patient fibroblasts demonstrated that the p.Arg91LysfsTer variant results in significantly lower levels of transcript compared to wild type. Based on the potential impact of frameshift variants and the supporting evidence from the literature, the p.Arg91LysfsTer14 variant is classified as pathogenic for disorders of intracellular cobalamin metabolism. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population.

Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 24599607, 19760748, 25687216, 32164588, 31681265, 24210589, 20631720, 23954310, 23837176, 21228398, 16311595, 25894566, 26979128, 27014578, 29302025, 26990548, 30712249, 29294253, 28835862, 31137025, 28481040, 27252276, 31497484, 31574870, 32071835, 31503356, 30157807, 31998365, 31980526, 31589614, 32943488, 33587123)

This variant was identified as compound heterozygous with NM_015506.3:c.658_660del._x000D_ Criteria applied: PVS1, PM3_VSTR, PP4

PVS1, PS3, PM3

The c.270_271insA;p.(Arg91Lysfs*14) is a null frameshift variant (NMD) in the MMACHC gene and predicts alteration of the nonsense-mediate decay - NMD is present in a relevant exon to the transcript - PVS1. This sequence change has been observed in affected individual(s) and ClinVar contains an entry for this variant (ClinVar ID: 1421; PMID: 16311595; PMID: 19760748; PMID: 20631720; PMID: 24599607; PMID: 25894566) - PS4. The variant is present at low allele frequencies population databases (rs398124292 – gnomAD 0.00008037%; ABraOM 0.003843 frequency - http://abraom.ib.usp.br/) - PM2_supporting. In summary, the currently available evidence indicates that the variant is pathogenic.

ACMG classification criteria: PVS1, PS4, PM3

Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as pathogenic. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0106 - This gene is known to be associated with autosomal recessive disease. (N) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (exon 2 of 4). (P) 0251 - Variant is heterozygous. (N) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (314 heterozygotes, 0 homozygotes). (P) 0701 - Comparable variants also predicted to result in NMD, have very strong previous evidence for pathogenicity in patients with Methylmalonic acidemia (Decipher, ClinVar). (P) 0801 - Strong previous evidence of pathogenicity in many unrelated individuals with Methylmalonic acidemia (LOVD, ClinVar, PMID: 31279840). (P) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign

This duplication causes a shift in the reading frame and is expected to result in the loss of a functional protein. Experimental evidence has demonstrated a significant reduction in transcript levels in the presence of this variant (PMID: 19370762). This variant has been identified homozygous and compound heterozygous in multiple individuals with clinical features associated with this gene, and has been reported as a common disease causing variant (PMID: 16311595, 19760748, 20631720, 24599607). The frequency of this variant in the general population is consistent with pathogenicity for a recessive disorder (http://gnomad.broadinstitute.org).This observation is not an independent occurrence and has been identified in the same individual by RCIGM, the other laboratory participating in the GEMINI study.

ACMG classification criteria: PVS1 very strong, PS4 strong, PM3 strong

The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.112%). This variant was predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. Multiple pathogenic variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000001421 / PMID: 16311595). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline.

PM3_very_strong, PS3, PVS1

This sequence change creates a premature translational stop signal (p.Arg91Lysfs*14) in the MMACHC gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in MMACHC are known to be pathogenic (PMID: 16311595). This variant is present in population databases (rs543840147, gnomAD 0.2%), and has an allele count higher than expected for a pathogenic variant. This premature translational stop signal has been observed in individual(s) with early onset cobalamin C deficiency (PMID: 16311595, 19760748, 20631720, 24599607, 25894566). ClinVar contains an entry for this variant (Variation ID: 1421). For these reasons, this variant has been classified as Pathogenic.

The observed frameshift variant c.271dup(p.Arg91LysfsTer14) in MMACHC gene has been reported previously in homozygous and compound heterozygous state in multiple individuals with cobalamin C disease (Wang C, et al., 2019, Guéant JL, et al., 2018). Experimental evidence has demonstrated a significant reduction in transcript levels in the presence of this variant (Lerner-Ellis JP, et al., 2009). The c.271dup variant is reported with 0.1% allele frequency in gnomAD Exomes. This variant has been reported to the ClinVar database as Uncertain Significance/Pathogenic (multiple submissions).This variant causes a frameshift starting with codon Arginine at 91, changes this aminoacid to Lysine residue, and creates a premature stop codon at position 14 of the new reading frame, denoted p.Arg91LysfsTer14. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Pathogenic.

MMACHC: PM3:Very Strong, PVS1, PM2:Supporting, PP4, PS3:Supporting

The MMACHC c.271dupA variant is predicted to result in a frameshift and premature protein termination (p.Arg91Lysfs*14). This variant is one of the most commonly reported pathogenic variants causative for methylmalonic acidemia and homocystinuria, cblC type (Lerner-Ellis et al. 2006. PubMed ID: 16311595; Richard et al. 2009. PubMed ID: 19760748). It has been interpreted as pathogenic by many outside laboratories (https://www.ncbi.nlm.nih.gov/clinvar/variation/1421/). This variant is reported in 0.28% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. Numerous other premature protein termination variants in MMACHC have been reported to be disease-causing (Human Gene Mutation Database). This variant is interpreted as pathogenic.

This individual is heterozygous for a pathogenic variant c.271dup in the MMACHC gene. This frameshifting variant is predicted to create a premature stop codon p.(Arg91Lysfs*14) and may result in a null allele due to nonsense-mediated mRNA decay. This variant is one of the most common variants associated with cblC type methylmalonic aciduria and homocystinuria (Lerner-Ellis et al 2006 Nat Genet 38:93-100). This variant is considered to be pathogenic according to the ACMG guidelines.

Accounts for approximately 30%-50% of disease alleles in individuals of European ancestry.