Submissions for variant NM_001048174.2(MUTYH):c.1333G>A (p.Ala445Thr)

gnomAD frequency: 0.00008  dbSNP: rs192816572

Total submissions: 13

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000130207	SCV000185045	uncertain significance	Hereditary cancer-predisposing syndrome	2023-03-07	criteria provided, single submitter	clinical testing	The p.A473T variant (also known as c.1417G>A), located in coding exon 14 of the MUTYH gene, results from a G to A substitution at nucleotide position 1417. The alanine at codon 473 is replaced by threonine, an amino acid with similar properties. This alteration has been reported in several patient cohorts including an early-onset colorectal cancer patient, an individual with greater than 5 colorectal adenomas, and an individual who underwent clinical genetic testing for Lynch syndrome; however, no other alterations in the MUTYH gene were detected in these cases, and p.A473T was classified as a variant of unknown significance (Fleischmann C et al. Int. J. Cancer. 2004 Apr;109:554-8; Olschwang S et al. Genet. Test. 2007;11:315-20; Yurgelun MB et al. Gastroenterology. 2015 Sep;149:604-13.e20). Functional studies of this variant demonstrate that it has near-wild type function in an E. coli-based complementation assay; however, glycosylase assays have never been conducted on this variant (Komine K et al. Hum. Mutat. 2015 Jul;36:704-11). Of note, this alteration is also designated as p.A459T in published literature. This amino acid position is not well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
GeneDx	RCV000656912	SCV000211418	uncertain significance	not provided	2023-09-19	criteria provided, single submitter	clinical testing	Published functional studies demonstrate normal base excision repair activity, but this variant may result in aberrant splicing (Komine et al., 2015; Yamada et al., 2019); In silico analysis supports a deleterious effect on splicing; In silico analysis supports that this missense variant does not alter protein structure/function; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 14991577, 25980754, 27498913, 17949294, 26332594, 16134146, 26269718, 19725997, 25186627, 31687339, 17031395, 25820570, 23108399, 15465463, 34816434)
Invitae	RCV000198237	SCV000254702	uncertain significance	Familial adenomatous polyposis 2	2024-02-01	criteria provided, single submitter	clinical testing	This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 473 of the MUTYH protein (p.Ala473Thr). This variant is present in population databases (rs192816572, gnomAD 0.008%). This missense change has been observed in individual(s) with clinical features of MUTYH-associated polyposis (PMID: 14991577, 17949294; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is also known as c.1375G>A (p.A459T). ClinVar contains an entry for this variant (Variation ID: 141614). 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 tolerated. Experimental studies have shown that this missense change does not substantially affect MUTYH function (PMID: 25820570). RNA analysis performed to evaluate the impact of this missense change on mRNA splicing indicates it does not significantly alter splicing (Invitae). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Color Diagnostics, LLC DBA Color Health	RCV000130207	SCV000685573	uncertain significance	Hereditary cancer-predisposing syndrome	2023-03-22	criteria provided, single submitter	clinical testing	This missense variant replaces alanine with threonine at codon 473 of the MUTYH protein. This variant is also known as c.1375G>A (p.Ala459Met) based on an alternative transcript (NM_001048171). Computational prediction is inconclusive regarding the impact of this variant on protein structure and function (internally defined REVEL score threshold 0.5 < inconclusive < 0.7, PMID: 27666373). Splice site prediction tools suggest that this variant may strengthen an alternative splice donor site. An RNA study using lymphoblastoid cell lines derived from a phenotypically normal subject has shown that this variant leads to the use of the alternative splice donor site (PMID: 31687339), creating a frameshift in the transcript. The clinical relevance of this observation is not known. A functional study has shown that this variant protein leads to similar base excision repair activity in comparison with the wild-type protein in a bacterial complementation assay (PMID: 25820570). This variant has been reported in individuals affected with Lynch syndrome-associated cancer and/or polyps (PMID: 25980754), multiple colorectal adenomas (PMID: 17949294), and breast cancer (PMID: 25186627). This variant has also been identified in 15/282886 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.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000212718	SCV000711961	uncertain significance	not specified	2019-01-15	criteria provided, single submitter	clinical testing	Variant classified as Uncertain Significance - Favor Benign. The p.Ala473Thr var iant in MUTYH has been reported in the heterozygous state in one individual with colorectal cancer (Fleischmann 2004) and one individual who was tested for a Ly nch Syndrome-associated cancer or colorectal polyps (Yurgelun 2015). Another stu dy reported this variant in an unspecified number of individuals with adenomatou s polyposis (Olschwang 2007; variant reported as Ala459Thr). In vitro functional studies provide some evidence that the p.Ala473Thr variant may not impact prote in function (Komine 2015). However, these types of assays may not accurately rep resent biological function. This variant has also been reported in ClinVar (Vari ation ID 141614) and in 0.02% (14/129192) of European chromosomes by gnomAD (htt p://gnomad.broadinstitute.org). Computational prediction tools and conservation analysis support that the p.Ala473Thr variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. In summary , while the clinical significance of the p.Ala473Thr variant is uncertain, these data suggest that it is more likely to be benign. ACMG/AMP criteria applied: BP 4, BS3_P.
Counsyl	RCV000198237	SCV000788479	uncertain significance	Familial adenomatous polyposis 2	2017-01-25	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000656912	SCV000806342	uncertain significance	not provided	2017-10-27	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000656912	SCV000888308	uncertain significance	not provided	2023-06-14	criteria provided, single submitter	clinical testing	In the published literature, this variant has been reported in individuals affected with colorectal cancer and/or polyps (PMID: 25980754 (2015), 17949294 (2007), 14991577 (2004)) or breast cancer (PMID: 25186627 (2015)). An experimental study suggested that this variant retained MUTYH functional activity in bacterial cells (PMID: 25820570 (2015)). However, another study detected aberrant splicing of MUTYH mRNA in a phenotypically normal individual carrying this variant (PMID: 31687339 (2019)). The frequency of this variant in the general population, 0.0002 (10/50820 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. 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. Additional analysis using software algorithms for the prediction of the effect of nucleotide changes on MUTYH mRNA splicing yielded predictions that this variant may result in the gain of a cryptic splice site without affecting the natural splice sites . Based on the available information, we are unable to determine the clinical significance of this variant.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000212718	SCV000917800	uncertain significance	not specified	2023-07-31	criteria provided, single submitter	clinical testing	Variant summary: MUTYH c.1417G>A (p.Ala473Thr) results in a non-conservative amino acid change located in the NUDIX hydrolase domain (IPR000086) and C-terminal domain (IPR029119) of the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. Additionally, several computational tools predict a significant impact on normal splicing: four predict the variant strengthens a cryptic 5' donor site. At least one publication reports experimental evidence supporting computational predictions that this variant affects mRNA splicing, finding that the variant resulted in the utilization of a cryptic 5' donor site, leading to a frameshift (p.Ala473PhefsX38; Yamada_2019). The variant allele was found at a frequency of 5.2e-05 in 251686 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in MUTYH causing MUTYH-Associated Polyposis (5.2e-05 vs 0.0046), allowing no conclusion about variant significance. c.1417G>A has been reported in the literature in individuals affected with colorectal, breast, and cervical cancer, however without strong evidence for causality (e.g., Fleischmann_2004, Olschwang_2007, Tung_2014, Yurgelun_2015, Barreiro_2022). These reports therefore do not provide unequivocal conclusions about association of the variant with MUTYH-associated Polyposis. One publication reports experimental evidence evaluating an impact on protein function, finding that the variant showed no damaging effect (e.g., Komine_2015). The following publications have been ascertained in the context of this evaluation (PMID: 16134146, 14991577, 25820570, 26332594, 17949294, 25186627, 25980754, 34816434, 31687339). Ten submitters have reported clinical-significance assessments for this variant to ClinVar after 2014. All submitters classified the variant as uncertain significance. Additionally, another variant disrupting the same codon, c.1418C>A (p.Ala473Asp), has been reported in the literature in individuals affected with Familial adenomatous polyposis, and the variant was found to segregate with disease in related individuals (PMID: 16134146); experimental studies also found the A473D variant to be functionally defective (PMIDs: 25820570, 16134146). Based on the evidence outlined above, the variant was classified as VUS-possibly pathogenic.
Illumina Laboratory Services, Illumina	RCV000198237	SCV001253574	uncertain significance	Familial adenomatous polyposis 2	2017-04-28	criteria provided, single submitter	clinical testing	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Fulgent Genetics, Fulgent Genetics	RCV002505107	SCV002816956	uncertain significance	Familial adenomatous polyposis 2; Gastric cancer	2021-07-20	criteria provided, single submitter	clinical testing
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000212718	SCV004024923	uncertain significance	not specified	2023-08-15	criteria provided, single submitter	clinical testing
Baylor Genetics	RCV000198237	SCV004198865	uncertain significance	Familial adenomatous polyposis 2	2023-09-19	criteria provided, single submitter	clinical testing