Submissions for variant NM_001048174.2(MUTYH):c.466C>T (p.Arg156Trp)

gnomAD frequency: 0.00002  dbSNP: rs779997419

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Ambry Genetics	RCV000167037	SCV000217861	uncertain significance	Hereditary cancer-predisposing syndrome	2023-03-02	criteria provided, single submitter	clinical testing	The p.R184W variant (also known as c.550C>T), located in coding exon 7 of the MUTYH gene, results from a C to T substitution at nucleotide position 550. The arginine at codon 184 is replaced by tryptophan, an amino acid with dissimilar properties. This alteration (designated as p.R170W) was previously identified in conjunction with MUTYH alteration p.Y104C in an individual with adenomatous polyposis and colorectal cancer; however, functional effect and phase of the variants were not determined (Gómez-Fernández N et al. BMC Med. Genet. 2009 Jun;10:57). In addition, this alteration was also identified in conjunction with a second MUTYH alteration, p.Tyr104*, in an individual diagnosed with either colon cancer or polyps at age 66; however, the phase was unknown (Ricci MT et al. J. Hum. Genet. 2017 Feb;62:309-315). This alteration was detected in a study of 1,165 individuals with a history of colorectal cancer or colon polyps as well as 590 controls (Gordon AS et al. Am J Hum Genet, 2019 Sep;105:526-533). This amino acid position is well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp	RCV000233436	SCV000285956	uncertain significance	Familial adenomatous polyposis 2	2024-01-13	criteria provided, single submitter	clinical testing	This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 184 of the MUTYH protein (p.Arg184Trp). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with clinical features of MUTYH-related conditions (PMID: 19531215, 27829682). This variant is also known as p.Arg170Trp. ClinVar contains an entry for this variant (Variation ID: 187318). 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. 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.
Counsyl	RCV000233436	SCV000487355	uncertain significance	Familial adenomatous polyposis 2	2016-05-10	criteria provided, single submitter	clinical testing
GeneDx	RCV000657000	SCV000566027	uncertain significance	not provided	2024-06-11	criteria provided, single submitter	clinical testing	Observed with a truncating MUTYH variant in individual(s) with colon polyps and cancer, but it is not known whether the variants occurred on the same (in cis) or on different (in trans) chromosomes (PMID: 27829682, 19531215); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as c.508C>T, p.Arg170Trp; This variant is associated with the following publications: (PMID: 27829682, 27498913, 19531215)
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000657000	SCV000601652	uncertain significance	not provided	2020-12-04	criteria provided, single submitter	clinical testing
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000485428	SCV000713011	uncertain significance	not specified	2017-03-06	criteria provided, single submitter	clinical testing	The p.Arg184Trp variant in MUTYH has been reported, along with a second MUTYH va riant of uncertain significance (phase unknown), in one Spanish individual with multiple adenomas and colorectal cancer (Gomez-Fernandez 2009) and has also been reported in ClinVar (Variation ID# 187318). In addition, this variant has been identified in 1/66738 of European chromosomes by the Exome Aggregation Consortiu m (ExAC, http://exac.broadinstitute.org; dbSNP rs779997419). Although the p.Arg1 84Trp variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. Computational prediction tools and conser vation analysis do not provide strong support for or against an impact to the pr otein. In summary, the clinical significance of the p.Arg184Trp variant is uncer tain.
Color Diagnostics, LLC DBA Color Health	RCV000167037	SCV000911726	uncertain significance	Hereditary cancer-predisposing syndrome	2022-12-15	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with tryptophan at codon 184 of the MUTYH protein. This variant is also known as c.508C>T (p.Arg170Trp) 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). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in two individuals with suspected familial polyposis (PMID: 19531215, 27829682) and one of whom also has a pathogenic MUTYH covariant (PMID: 27829682). This variant has been identified in 3/246270 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000485428	SCV001361133	uncertain significance	not specified	2019-10-10	criteria provided, single submitter	clinical testing	Variant summary: MUTYH c.550C>T (p.Arg184Trp) results in a non-conservative amino acid change located in the HhH-GPD domain of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.2e-05 in 251460 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.550C>T has been reported in the literature in individual with multiple adenomas and colorectal cancer (Gomez-Fernandez_2009) and in an individual suspected of MAP (Ricci_2016), both without strong evidence of causality. These reports do not provide unequivocal conclusions about association of the variant with MUTYH-associated Polyposis. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Seven clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.
St. Jude Molecular Pathology, St. Jude Children's Research Hospital	RCV001526816	SCV001737463	uncertain significance	Familial multiple polyposis syndrome	2021-05-13	criteria provided, single submitter	clinical testing	The MUTYH c.466C>T (p.Arg156Trp) missense change has a maximum subpopulation frequency of 0.0031% in gnomAD v2.1.1 (PM2_supporting; https://gnomad.broadinstitute.org/variant/1-45798461-G-A?dataset=gnomad_r2_1). Seven of seven in silico tools predict a deleterious effect of this variant on protein function (PP3), but to our knowledge these predictions have not been confirmed by functional assays. This variant has been reported in two individuals with colorectal cancer who both had a second variant in MUTYH, one classified as pathogenic and one classified as of uncertain significance (PMID: 27829682, 19531215). In both individuals, the phase of the variants (in cis or in trans) was not known (PM3_supporting). In summary, this variant meets criteria to be classified as of uncertain significance based on the ACMG/AMP criteria: PM2_supporting, PM3_supporting, PP3.
Baylor Genetics	RCV000233436	SCV004198851	uncertain significance	Familial adenomatous polyposis 2	2023-09-30	criteria provided, single submitter	clinical testing
All of Us Research Program, National Institutes of Health	RCV000233436	SCV004837367	uncertain significance	Familial adenomatous polyposis 2	2023-10-02	criteria provided, single submitter	clinical testing	This missense variant replaces arginine with tryptophan at codon 184 of the MUTYH protein. This variant is also known as c.508C>T (p.Arg170Trp) 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). To our knowledge, functional studies have not been reported for this variant. This variant has been reported in two individuals with suspected familial polyposis (PMID: 19531215, 27829682) and one of whom also has a pathogenic MUTYH covariant (PMID: 27829682). This variant has been identified in 3/246270 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.