Shifting landscapes of human MTHFR missense-variant effects

Abstract

Most rare clinical missense variants cannot currently be classified as pathogenic or benign. Deficiency in human 5,10-methylenetetrahydrofolate reductase (MTHFR), the most common inherited disorder of folate metabolism, is caused primarily by rare missense variants. Further complicating variant interpretation, variant impacts often depend on environment. An important example of this phenomenon is the MTHFR variant p.Ala222Val (c.665C>T), which is carried by half of all humans and has a phenotypic impact that depends on dietary folate. Here we describe the results of 98,336 variant functional-impact assays, covering nearly all possible MTHFR amino acid substitutions in four folinate environments, each in the presence and absence of p.Ala222Val. The resulting atlas of MTHFR variant effects reveals many complex dependencies on both folinate and p.Ala222Val. MTHFR atlas scores can distinguish pathogenic from benign variants and, among individuals with severe MTHFR deficiency, correlate with age of disease onset. Providing a powerful tool for understanding structure-function relationships, the atlas suggests a role for a disordered loop in retaining cofactor at the active site and identifies variants that enable escape of inhibition by S-adenosylmethionine. Thus, a model based on eight MTHFR variant effect maps illustrates how shifting landscapes of environment-and genetic-background-dependent missense variation can inform our clinical, structural, and functional understanding of MTHFR deficiency.

Exome-Wide Association Study Identifies East Asian-Specific Missense Variant MTHFR C136T Influencing Homocysteine Levels in Chinese Populations RH: ExWAS of tHCY in a Chinese Population

“…This C136T variant was in weak linkage disequilibrium (LD) with the C677T variant ( r 2 = 0.014). A previous enzyme kinetics experiment has shown that the arginine to tryptophan substitution at C136T led to a reduced enzymatic activity of MTHFR , which provided direct evidence for a functional role of this variant, consistent with our observation of the presence of multiple causal mutations at this locus ( Tan et al, 2021 ; Weile et al, 2021 ). A haplotype analysis further showed that these two alleles (677T and 136T) together affect tHCY in a compound heterozygote manner ( Figure 4 ).…”

Improved pathogenicity prediction for rare human missense variants

“…It has become possible to experimentally assess the functional impact of nearly all possible missense variants for a target protein, yielding “deep mutational scans” or “variant effect maps.” 3 , 4 , 5 , 6 , 7 , 8 , 9 , 10 , 11 , 12 , 13 However, the MaveDB 14 resource currently contains variant effect maps for fewer than 1% of the ∼4,000 human disease-associated proteins, and a high-quality fully-comprehensive experimental atlas of functional missense variation could be decades away.…”

Variants in ASPH cause exertional heat illness and are associated with malignant hyperthermia susceptibility

“…Rare variation is reported in gnomAD for many junctin encoded amino acids residues outside of the KEKE motifs, thus making it critical to define which changes are likely pathogenic and which are not. An approach that combines variant scanning 44 with functional validation, if a suitable high throughput assay can be established, is an attractive strategy for evaluating the potential pathogenicity of other junctin variants.…”