rs750592289
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 7P and 1B. PM1PM2PM5PP5BP4
The NM_001048174.2(MUTYH):c.469C>T(p.Arg157Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000015 in 1,461,886 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R157Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001048174.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MUTYH | NM_001048174.2 | c.469C>T | p.Arg157Trp | missense_variant | 7/16 | ENST00000456914.7 | NP_001041639.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MUTYH | ENST00000456914.7 | c.469C>T | p.Arg157Trp | missense_variant | 7/16 | 1 | NM_001048174.2 | ENSP00000407590.2 | ||
ENSG00000288208 | ENST00000671898.1 | n.1057C>T | non_coding_transcript_exon_variant | 11/21 | ENSP00000499896.1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251446Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135916
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461886Hom.: 0 Cov.: 36 AF XY: 0.0000138 AC XY: 10AN XY: 727246
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Familial adenomatous polyposis 2 Uncertain:3
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 26, 2024 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Jun 26, 2023 | This missense variant replaces arginine with tryptophan at codon 185 of the MUTYH protein. 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). Functional studies have shown that this variant has no detectable glycosylase activity and reduced substrate binding (PMID: 19953527, 20418187). This variant has been reported in individuals affected with colorectal cancer and polyposis (PMID: 18091433) or breast cancer (PMID: 32658311). This variant has been identified in 2/251446 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 10, 2023 | This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 185 of the MUTYH protein (p.Arg185Trp). 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. Experimental studies have shown that this missense change affects MUTYH function (PMID: 19953527, 20418187, 22252118). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Not Available". The tryptophan amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 419386). This missense change has been observed in individual(s) with polyposis, colorectal cancer, and/or breast cancer (PMID: 18091433, 32658311). This variant is present in population databases (rs750592289, gnomAD 0.004%). - |
not provided Pathogenic:2
Likely pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Nov 12, 2019 | Not observed at a significant frequency in large population cohorts (Lek 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Also known as c.511C>T, p.Arg171Trp; This variant is associated with the following publications: (PMID: 19953527, 25820570, 18091433, 20418187, 25638157, 32658311) - |
Likely pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2018 | - - |
Hereditary cancer-predisposing syndrome Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Mar 22, 2023 | This missense variant replaces arginine with tryptophan at codon 185 of the MUTYH protein. 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). Functional studies have shown that this variant has no detectable glycosylase activity and reduced substrate binding (PMID: 19953527, 20418187). This variant has been reported in individuals affected with colorectal cancer and polyposis (PMID: 18091433) or breast cancer (PMID: 32658311). This variant has been identified in 2/251446 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. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 07, 2024 | The p.R185W variant (also known as c.553C>T), located in coding exon 7 of the MUTYH gene, results from a C to T substitution at nucleotide position 553. The arginine at codon 185 is replaced by tryptophan, an amino acid with dissimilar properties. This alteration was first reported in a male patient with colon cancer at age 49 and 90-100 polyps (Cattaneo F et al Genet. Med. 2007 Dec; 9(12):836-41). One functional analysis of this alteration using human proteins from a bacterial system suggests this alteration results in severe reduction in binding affinity as well as reduced adenine removal activity compared to the wild-type protein (D'Agostino VG et al DNA Repair (Amst.). 2010 Jun; 9(6):700-7). An additional study in which this alteration was expressed in Mutyh-/- mouse defective cells showed dysfunctional Base Excision Repair and goes on to suggest that the mutant protein produced by this alteration revealed a more pronounced phenotype than the simple loss of the Mutyh protein, suggesting a sort of dominant-negative effect (Molatore S et al Hum. Mutat. 2010 Feb; 31(2):159-66). Of note, this alteration is also designated as p.R171W (c.511C>T) in some published literature. This amino acid position is highly 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. - |
Breast carcinoma Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Medical Genetics Laboratory, Umraniye Training and Research Hospital, University of Health Sciences | Sep 10, 2021 | - - |
Familial cancer of breast Uncertain:1
Uncertain significance, no assertion criteria provided | research | Center of Medical Genetics and Primary Health Care | Jul 15, 2020 | ACMG Guidelines 2015 criteria The MUTYH gene variant p.Arg185Trp is in exon 7 and in the HhH-GPD domain (V118-249W aa) with a function in base-excision repair (PMID: 10706276). Experimental studies showed this missense change abolishes the glycosylase activity of the MUTYH protein (PMID: 20418187, 19953527) (PS3 Pathogenic Strong). It is in a mutation hotspot of 7 pathogenic, including missense pathogenic variants (PM1 Pathogenic Moderate). The allele frequency in GnomAD exomes is 0.00000795 which is less the threshold 0.0001 for recessive gene MUTYH, and the variant is not found in GnomAD genomes (PM2 Pathogenic Moderate). Meantime, majority of missense variants detected in MUTYH are pathogenic and known cause of disease (PP2 Pathogenic Supporting). In our study this variant was found in a 54-year-old female patient with unilateral breast cancer and a family history of cancer. Based on the evidence above we classified this variant as a Variant of Unknown Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at