ClinVar Genomic variation as it relates to human health

This variant is denoted MUTYH c.254A>G at the cDNA level, p.His85Arg (H85R) at the protein level, and results in the change of a Histidine to an Arginine (CAT>CGT). This variant was observed in the homozygous state in a patient who had a history of 10-100 colorectal adenomas and a sibling with colorectal cancer (Morak 2010). MUTYH His85Arg was not observed at a significant frequency in large population cohorts (NHLBI Exome Sequencing Project, The 1000 Genomes Consortium 2015, Lek 2016). Since Histidine and Arginine share similar properties, this is considered a conservative amino acid substitution. MUTYH His85Arg occurs at a position that is conserved across species and is not located in a known functional domain. In silico analyses predict that this variant is probably damaging to protein structure and function. Based on the currently available evidence and internal data, we consider MUTYH His85Arg to be a likely pathogenic variant. Of note, MUTYH-Associated Polyposis (MAP) is a recessive condition associated with two pathogenic variants on opposite chromosomes in MUTYH.

The p.H85R variant (also known as c.254A>G), located in coding exon 3 of the MUTYH gene, results from an A to G substitution at nucleotide position 254. The histidine at codon 85 is replaced by arginine, an amino acid with highly similar properties. This variant has been identified in the homozygous state and likely in trans with a MUTYH pathogenic variant in individuals diagnosed with clinical features of MUTYH-associated polyposis (MAP) (Morak M et al. Clin Genet, 2010 Oct;78:353-63; Interlaboratory communication). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the majority of available evidence to date, this variant is likely to be pathogenic.

Variant summary: MUTYH c.254A>G (p.His85Arg) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 8e-06 in 251476 control chromosomes. c.254A>G has been reported in the literature in one homozygous individual affected with 10-100 colorectal adenomas and a sibling affected with colorectal cancer (Morak_2010). Additionally, the variant was also reported in one individual with MUTYH-Associated Polyposis (Sutcliffe_2019). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Four ClinVar submitters (evaluation after 2014) cite the variant as uncertain significance (n=3) and likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.

This missense variant replaces histidine with arginine at codon 85 of the MUTYH protein. This variant is also known as c.212A>G (p.His71Arg) based on an alternative transcript (NM_001048171). Computational prediction suggests that this variant may not impact protein structure and function (internally defined REVEL score threshold <= 0.5, PMID: 27666373). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in the homozygous state in an individual affected with colon adenomas (PMID: 20618354). This variant has also been identified in 2/251476 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

The frequency of this variant in the general population, 0.000008 (2/251476 chromosomes, http://gnomad.broadinstitute.org), is uninformative in assessment of its pathogenicity. In the published literature, the variant has been reported in an individual with MUTYH-Associated Polyposis (PMID: 30604180 (2019)). Additionally, the variant was reported in a family with a history of polyps and colorectal cancer (PMID: 20618354 (2010)). Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is deleterious or benign. Based on the available information, we are unable to determine the clinical significance of this variant.

ClinVar contains an entry for this variant (Variation ID: 234004). For these reasons, this variant has been classified as Pathogenic. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. This missense change has been observed in individuals with colorectal polyposis (PMID: 20618354; Invitae). It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs558707786, gnomAD 0.007%). This sequence change replaces histidine, which is basic and polar, with arginine, which is basic and polar, at codon 85 of the MUTYH protein (p.His85Arg).

The MUTYH p.His85Arg variant was not identified in the literature nor was it identified in the following databases: Cosmic, MutDB, Insight Colon Cancer Gene Variant Database. The variant was identified in dbSNP (ID: rs558707786) as “With Uncertain significance allele”,ClinVar (1x as uncertain significance by Ambry Genetics), and Clinvitae (1x as uncertain significance). The variant was identified in control databases in 2 of 246258 chromosomes at a frequency of 0.000008 in the following populations: African in 1 of 15304 chromosomes (freq. 0.000065), and Other in 1 of 5486 chromosomes (freq. 0.00018) (Genome Aggregation Consortium Feb 27, 2017). The p.His85Arg residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. The variant occurs outside of the splicing consensus sequence and 1 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.