rs34126013
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PM5PP3_ModeratePP5_Very_Strong
The NM_001048174.2(MUTYH):c.637C>T(p.Arg213Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000235 in 1,613,978 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R213Q) has been classified as Likely pathogenic.
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000024 ( 0 hom. )
Consequence
MUTYH
NM_001048174.2 missense
NM_001048174.2 missense
Scores
15
3
1
Clinical Significance
Conservation
PhyloP100: 6.13
Genes affected
MUTYH (HGNC:7527): (mutY DNA glycosylase) This gene encodes a DNA glycosylase involved in oxidative DNA damage repair. The enzyme excises adenine bases from the DNA backbone at sites where adenine is inappropriately paired with guanine, cytosine, or 8-oxo-7,8-dihydroguanine, a major oxidatively damaged DNA lesion. The protein is localized to the nucleus and mitochondria. This gene product is thought to play a role in signaling apoptosis by the introduction of single-strand breaks following oxidative damage. Mutations in this gene result in heritable predisposition to colorectal cancer, termed MUTYH-associated polyposis (MAP). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2017]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 16 ACMG points.
PM1
In a hotspot region, there are 7 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 16 uncertain in NM_001048174.2
PM2
Very rare variant in population databases, with high coverage;
PM5
Other missense variant is known to change same aminoacid residue: Variant chr1-45332457-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 406867.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.909
PP5
Variant 1-45332458-G-A is Pathogenic according to our data. Variant chr1-45332458-G-A is described in ClinVar as [Likely_pathogenic]. Clinvar id is 185274.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-45332458-G-A is described in Lovd as [Pathogenic]. Variant chr1-45332458-G-A is described in Lovd as [Likely_pathogenic]. Variant chr1-45332458-G-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| MUTYH | NM_001048174.2 | c.637C>T | p.Arg213Trp | missense_variant | 9/16 | ENST00000456914.7 | NP_001041639.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| MUTYH | ENST00000456914.7 | c.637C>T | p.Arg213Trp | missense_variant | 9/16 | 1 | NM_001048174.2 | ENSP00000407590.2 | ||
| ENSG00000288208 | ENST00000671898.1 | n.1225C>T | non_coding_transcript_exon_variant | 13/21 | ENSP00000499896.1 |
Frequencies
GnomAD3 genomes 0.0000197 AC: 3AN: 152220Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000679 AC: 17AN: 250364Hom.: 0 AF XY: 0.0000590 AC XY: 8AN XY: 135610
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GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461758Hom.: 0 Cov.: 36 AF XY: 0.0000234 AC XY: 17AN XY: 727174
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GnomAD4 genome 0.0000197 AC: 3AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74356
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:17
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Pathogenic:8
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Oct 24, 2022 | Published functional studies demonstrate a damaging effect: deficient in glycosylase activity and partially deficient in base excision repair activity (Bai et al., 2005; Komine et al., 2015); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Also known as c.679C>T p.(Arg227Trp); This variant is associated with the following publications: (PMID: 15366000, 15673720, 19506731, 28127763, 30604180, 32923906, 17931073, 25820570, 21171015, 14991577, 27194394, 27799157, 20663686, 23605219, 23507534, 24470512, 28533537, 28152038, 32338768, 33258288, 30787465, 30613976, 23108399, 11801590, 34704405, 23561487) - |
| Pathogenic, no assertion criteria provided | clinical testing | Department of Pathology and Laboratory Medicine, Sinai Health System | - | The MUTYH p.Arg241Trp variant was identified in 2 of 822 proband chromosomes from individuals with colorectal adenomas (Isidro 2004, Fleischmann 2004). In both cases the variant occurred as a biallelic mutation in combination with the pathogenic MUTYH p.Gly382Asp mutation. The p.Arg241Trp variant was also identified in dbSNP (ID: rs34126013), HGMD, UMD (4X as a causal variant), and the “InSiGHT Colon Cancer Database”. The p.Arg241 residue is conserved across mammals and more distantly related organisms and 5/5 computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest that the p.Arg241Trp variant may impact the protein. In addition, one functional study found the variant to be severely defective in A/8-oxoG binding and glycosylase activities, and it failed to complement MutY-deficiency in E.coli (Bai 2005). In summary, based on the above information, this variant meets our laboratory’s criteria to be classified as pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2023 | MUTYH: PM3:Strong, PS3, PM2, PP3 - |
| Pathogenic, no assertion criteria provided | clinical testing | Clinical Genetics, Academic Medical Center | - | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Oct 05, 2023 | The MUTYH c.721C>T (p.Arg241Trp) variant has been reported in the published literature in the compound heterozygous or homozygous state in multiple individuals with polyposis and/or colorectal cancer (PMID: 28533537 (2017), 27194394 (2016), 24470512 (2014), 23561487 (2013), 15366000 (2004)). It has also been reported in individuals with prostate cancer (PMID: 32338768 (2020)) and breast cancer (PMIDs: 30564557 (2018) and 33313162 (2020)), as well as in a breast cancer case and control individuals in a large scale breast cancer association study (PMID: 33471991 (2021), see also LOVD (http://databases.lovd.nl/shared/genes/MUTYH)). Experimental studies indicate that the variant is damaging to MUTYH protein function (PMIDs: 25820570 (2015) and 15673720 (2005)). The frequency of this variant in the general population, 0.00026 (8/30604 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 predictions that this variant is damaging. Based on the available information, this variant is classified as pathogenic. - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Clinical Genetics and Genomics, Karolinska University Hospital | Jun 16, 2015 | - - |
| Pathogenic, no assertion criteria provided | clinical testing | Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) | - | - - |
Familial adenomatous polyposis 2 Pathogenic:7
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 13, 2024 | - - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jun 14, 2016 | The c.721C>T (p.Arg241Trp) variant, also referred to as c.679C>T (p.Arg227Trp), has been reported in five studies in which it is found in a total of six MYH-associated polyposis patients, including two siblings in a homozygous state and four patients in a compound heterozygous state with one of the common pathogenic MUTYH missense variants (Isidro et al. 2004; Fleischmann et al. 2004; Bai et al. 2005; Torrezan et al. 2013; Guarinos et al. 2014). The variant was absent from 354 controls (Fleischmann et al. 2004) but is reported at a frequency of 0.00042 in the South Asian population of the Exome Aggregation Consortium. Functional studies demonstrated that the p.Arg241Trp variant has a severe defect in adenine (A) /7,8-dihydro-8-oxo-guanine binding and therefore in the ability to catalyze adenine excision from A/GO mismatches, one of the main functions of the protein. The p.Arg241Trp variant was also shown to have no detectable glycosylase activity and failed to complement mut Y-deficiency in E. coli. The variant does not affect binding to the hMSH2/hMSH6 complex (Bai et al. 2005; Komine et al. 2015). Based on the collective evidence, the p.Arg241Trp variant is classified as likely pathogenic for MYH-associated polyposis. - |
| Pathogenic, criteria provided, single submitter | clinical testing | All of Us Research Program, National Institutes of Health | Dec 13, 2023 | This missense variant replaces arginine with tryptophan at codon 241 of the MUTYH protein. This variant is also known as c.679C>T (p.Arg227Trp) based on an alternative transcript (NM_001048171). Computational prediction tool suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >=0.7, PMID: 27666373). Splice site prediction tools suggest that this variant may not impact RNA splicing. Functional studies have shown that this variant disrupts MUTYH protein function (PMID: 15673720, 25820570). This variant has been reported as compound heterozygous with another pathogenic variant in multiple individuals affected with polyposis and/or colorectal cancer (PMID: 14991577, 15366000, 24470512, 27194394, 28533537, Color internal data), and as homozygous in two siblings affected with attenuated polyposis (parents were consanguineous) (PMID: 23561487). This variant has been identified in 18/281720 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Likely Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | MUTYH p.Arg241Trp: This sequence change replaces arginine with tryptophan at codon 241 of the MUTYH protein (p.Arg241Trp). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and tryptophan. This variant is present in population databases (rs34126013, ExAC 0.04%). This variant has been reported as heterozygous with another pathogenic variant in MUTYH in multiple individuals affected with polyposis and/or colorectal cancer (PMID: 24470512, 14991577, 27194394), and as homozygous in two siblings from a family affected with polyposis (PMID: 23561487). ClinVar contains an entry for this variant (Variation ID: 185274). In addition, in-silico prediction for this alteration shows pathogenic computational verdict based on 12 pathogenic predictions from BayesDel_addAF, DANN, DEOGEN2, EIGEN, FATHMM-MKL, LIST-S2, M-CAP, MVP, MutationAssessor, MutationTaster, REVEL and SIFT vs 1 benign prediction from PrimateAI. Experimental studies suggest that this missense change disrupts MUTYH protein function in vitro and in a bacteria-based functional assay (PMID: 15673720, 25820570). Therefore, this variant has been classified as Likely Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Mendelics | Jul 02, 2018 | - - |
| Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Jan 04, 2017 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 28, 2024 | This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 241 of the MUTYH protein (p.Arg241Trp). This variant is present in population databases (rs34126013, gnomAD 0.03%). This missense change has been observed in individuals with colorectal cancer and/or polyposis (PMID: 14991577, 23561487, 24470512, 27194394). This variant is also known as c.679C>T (p.Arg227Trp). ClinVar contains an entry for this variant (Variation ID: 185274). 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. Experimental studies have shown that this missense change affects MUTYH function (PMID: 15673720, 25820570). This variant disrupts the p.Arg241 amino acid residue in MUTYH. Other variant(s) that disrupt this residue have been observed in individuals with MUTYH-related conditions (PMID: 19732775; Invitae), which suggests that this may be a clinically significant amino acid residue. For these reasons, this variant has been classified as Pathogenic. - |
Hereditary cancer-predisposing syndrome Pathogenic:2
| Pathogenic, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Sep 08, 2023 | This missense variant replaces arginine with tryptophan at codon 241 of the MUTYH protein. This variant is also known as c.637C>T (p.Arg213Trp) based on an alternative transcript (NM_001048174.2). Computational prediction tool suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >=0.7, PMID: 27666373). Functional studies have shown that this variant was deficient in A/8-oxoG binding and glycosylase activities , and failed to complement mutY-deficiency in Escherichia coli (PMID: 15673720, 25820570). This variant has been reported as biallelic with another pathogenic variant in multiple individuals affected with polyposis and/or colorectal cancer (PMID: 15366000, 19394335, 23561487, 24470512, 27194394, 28533537, 34704405). This variant has been identified in 18/281720 chromosomes in the general population by the Genome Aggregation Database (gnomAD). Based on the available evidence, this variant is classified as Pathogenic. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 14, 2021 | The p.R241W pathogenic mutation (also known as c.721C>T), located in coding exon 9 of the MUTYH gene, results from a C to T substitution at nucleotide position 721. The arginine at codon 241 is replaced by tryptophan, an amino acid with dissimilar properties. This alteration has been reported in conjunction with the common MUTYH founder mutations p.G396D (p.G382D) and p.Y179C (p.Y165C), other pathogenic/likely pathogenic MUTYH variants, and as homozygous in multiple patients with classic polyposis, attenuated polyposis, and/or colorectal cancer (Isidro G et al. Hum Mutat. 2004 Oct;24(4):353-4; Bai H et al. Nucleic Acids Res. 2005 Jan 26;33(2):597-604; Torrezan GT et al. Orphanet J Rare Dis. 2013 ;8:54; Guarinos C et al. Clin Cancer Res. 2014 Mar 1;20(5):1158-68; Win AK et al. Int J Cancer. 2016 Oct 1;139(7):1557-63; Khan N et al. Sci Rep. 2017 May 22;7(1):2214; Ambry internal data). Furthermore, the aforementioned co-occurrences are likely to be in trans due to multiple observances with different pathogenic or likely pathogenic MUTYH variants. In functional assays measuring glycosylase activity and DNA-binding activity, this variant demonstrated impaired protein function similar to the p.Y179C (p.Y165C) MUTYH founder mutation (Bai H et al. Nucleic Acids Res. 2005 Jan 26;33(2):597-604; Komine K et al. Hum Mutat. 2015 Jul;36(7):704-11). This alteration has also been identified in individuals diagnosed with male breast cancer, breast cancer and prostate cancer (Rizzolo P et al. Front Oncol, 2018 Dec;8:583; Lang GT et al. Ann Transl Med, 2020 Nov;8:1417; Nguyen-Dumont T et al. Int J Cancer, 2020 10;147:2142-2149). Of note, this alteration is also designated as p.R227W in published literature. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Uncertain
.;.;.;.;.;D;.;.;.;D;.;D
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
.;D;.;D;D;D;D;D;D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
.;.;.;.;.;H;.;.;.;.;.;.
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D
REVEL
Pathogenic
Sift
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D
Sift4G
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D
Polyphen
1.0
.;.;.;.;.;D;D;.;D;.;.;.
Vest4
MVP
MPC
0.56
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at