ClinVar Genomic variation as it relates to human health

This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].

The c.934-2A>G variant in MUTYH has been widely studied in the East Asian population and reported in at least 7 individuals with colorectal cancer; however, to our knowledge, none of these individuals had a second pathogenic germline MUTYH variant identified (Miyaki 2005 PMID:15890374, Kim 2007 PMID:17703316, Taki 2016 PMID:26684191). It has been identified in 1.54% (307/19952) of East Asian chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org). This variant has also been reported in ClinVar (Variation ID 41766). This variant occurs within the canonical splice site (+/- 1,2) and is predicted to cause altered splicing leading to an abnormal or absent protein. Functional studies was demonstrated to cause aberrant splicing in in vitro studies (Tao 2004 PMID:15180946, Taki 2016 PMID:26684191), but whether this alteration causes a biological loss of function of the MUTYH protein in humans is uncertain. In summary, while the predicted functional impact of this variant and in vitro studies favor a pathogenic role, based on the absence of reported affected individuals carrying this variant and a second pathogenic MUTYH variant in the literature despite its high frequency in the general population, its clinical significance is uncertain. Additional studies are needed to clarify the significance of this variant. ACMG/AMP Criteria applied: BS1_Supporting.

Variant summary: MUTYH c.934-2A>G is located in a canonical splice-site and is predicted to affect mRNA splicing resulting in a significantly altered protein due to either exon skipping, shortening, or inclusion of intronic material. Several computational tools predict a significant impact on normal splicing: four predict the variant abolishes the canonical 3' splicing acceptor site, while two predict the variant creates a novel 3' acceptor site, 9 nucleotides downstream from the original splice site. Earlier RNA studies reported that this variant affects mRNA splicing, resulting in the out-of-frame inclusion of intron 10, causing a premature translation stop signal (Tao_2004, Taki_2016, Thibodeau_2019), in addition, an abnormal splicing event removing 9 bp from the 5' end of exon 11 was also described (Taki_2016, Thibodeau_2019). However, a recent detailed analysis (Hernandez_2022) demonstrated that the out-of-frame inclusion of intron 10 is a naturally occurring, low-level alternative splicing event (detected in both variant carrier and control samples, in about 5-13% of transcripts), while the variant exclusively results in the in-frame deletion of 9 nucleotides from the 5' end of exon 11 (detected in about 22-29% of the transcripts). This deletion causes an in-frame loss of three amino acids (p.V312_Q314del), which is not located to any known domains (InterPro), but is predicted to be positioned within a flexible linker region between domains, which does not engage in any apparent specific interactions (Hernandez_2022). The variant allele was found at a frequency of 0.0012 in 253188 control chromosomes (gnomAD and publication data), predominantly at a frequency of 0.015 within the East Asian subpopulation (in the gnomAD database), including 5 homozygotes. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 3-fold of the estimated maximal expected allele frequency for a pathogenic variant in MUTYH causing MUTYH-Associated Polyposis (MAP) phenotype (0.0046). In addition, this variant was found at an even higher allele frequency in two Japanese control databases, jMorp and HGVD-Kyoto, with allele frequencies of 0.0195 and 0.0248, respectively. These data suggest that this variant is a benign polymorphism found primarily in populations of East Asian origin. c.934-2A>G has been reported in the literature in multiple individuals affected with colorectal polyposis, and other tumor phenotypes, including e.g. breast-, ovarian-, gallbladder-, colon-, endometrial- and thyroid cancer (e.g. Miyaki_2005, Kim_2007, Frey_2015, Hirotsu_2015, Taki_2016, Hansen_2017, Li_2017, Zhang_2017, Chan_2018, Thibodeau_2019, Wang_2019, Slavin_2020). However, none of the reported individuals with colorectal polyposis were indicated to be compound heterozygotes or homozygotes for MUTYH mutations. A recent case-control study in the Japanese population identified the variant in heterozygous state at a high frequency in both controls and colorectal cancer (CRC) cases, and found it in homozygous CRC patients (4 cases) who did not have multiple polyps, indicating that the variant is likely to be non-causative (Fujita_2020). A recent study also noted the lack of a polyposis phenotype in three biallelic carriers (Hernandez_2022). We also ascertained two studies reporting homozygous occurrences of the variant in a patient diagnosed with gastric cancer, and in a patient with endometrial cancer, without strong evidence of causality (Tao_2004, Wang_2019). A publication (Jian_2017) reported two independent breast cancer patients who did not carry the variant of interest, while some of their unaffected daughters (younger than the average age of onset for breast cancer) carried the variant. In addition, in a recent large study evaluating breast cancer cases and controls in the Breast Cancer Association Consortium (BCAC), the variant was reported in 253/60466 cases (allele frequency of 0.001) and 236/53461 controls (frequency 0.0011) (Dorling_2021, through LOVD). Other case-control studies indicated that this variant may be associated with moderate increase in risk for colorectal cancer in carriers (Tao_2008, Yang_2013), however larger studies will be necessary to clarify any such risk associations. Several co-occurrences with pathogenic variants have been reported in patients with associated penetrant phenotypes of familial adenomatous polyposis (FAP), breast- and colorectal cancer [APC c.2751delT, p.D917fs (Kohda_2016); BRCA1 c.2110_2111delAA, p.N704CfsX7 (Yang_2015); APC with an unspecified deletion (Li_2017); BRCA2 c.774_775delAA, p.Glu260Serfs*15 (Chan_2018); MLH1 c.704_723del, p.Lys236Glufs*64 (Chan_2018)]. An earlier functional study has suggested that the variant results in a mutant protein which is mislocalized in cells after transfection (Tao_2004), however, the authors analyzed a protein product resulting from the out-of-frame inclusion of intron 10, which lost the C-terminal NLS, therefore these results doesn't allow conclusions for the effect of the del9 transcript (Hernandez_2022), which is predicted to lead to an in-frame loss of three amino acids in a noncritical domain of the protein (p.V312_Q314del). The following publications have been ascertained in the context of this evaluation (PMID: 30093976, 28526081, 33471991, 26296696, 33309985, 28195393, 34716202, 26436112, 29093764, 17703316, 26837502, 22641385, 24733792, 28251689, 26824983, 15890374, 34897210, 27443514, 31575519, 26684191, 18271935, 15180946, 30833417, 30982232, 30886832, 24377541, 25927356, 28135145, 28445943). Multiple clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as pathogenic (n=1), likely pathogenic (n=2), uncertain significance (n=7), likely benign (n=5). Based on the evidence outlined above, the variant was classified as likely benign.

See Variant Classification Assertion Criteria.

This variant occurs at a canonical splice-acceptor site and is predicted to interfere with normal MUTYH mRNA splicing. Functional studies report that this variant results in aberrant transcripts (PMIDs: 15180946 (2004), 26684191 (2016) 30833417 (2019)), however, a recent RNA study demonstrates this variant exclusively results in the in-frame deletion of three amino acids and is unlikely to cause a significant effect on protein function (PMID: 34716202 (2022)). The frequency of this variant in the general population, 0.015 (223/14422 chromosomes in Other East Asian subpopulation, http://gnomad.broadinstitute.org), is higher than would generally be expected for pathogenic variants in this gene. In the published literature, the variant has been reported in individuals with colorectal polyps (PMID: 28251689 (2017), 29330641 (2018), 34716202 (2022)), colorectal cancer (PMID: 33563768 (2022), 34716202 (2022), 35098669 (2022)), breast cancer (PMID: 34716202 (2022), 35264596 (2022), 36119527 (2022)), familial adenomatous polyposis (FAP) (PMID: 17703316 (2007), 26837502 (2016)), as well as other cancer types. This variant is also reported in unaffected individuals (PMID: 28332257 (2017), 33309985 (2020), 33471991 (2021), https://databases.lovd.nl/shared/variants/MUTYH). Based on the available information, we are unable to determine the clinical significance of this variant.

The MUTYH c.934-2A>G variant (rs77542170), also known as IVS10-2A>G or c.892-2A>G for NM_001048171, is reported in the literature in multiple individuals with colorectal adenomatous polyposis or colorectal cancer, but has only been reported in the heterozygous state with no additional MUTYH variant identified (Hansen 2017, Taki 2016, Zhang 2017). This variant has also been reported heterozygously in individuals with breast and/or ovarian cancer (Hirotsu 2015, Kurian 2014) as well as an individual with glioma (Kline 2016). This variant is found heterozygously at a similar frequency in individuals with gastric cancer as in controls (Tao 2004). This variant disrupts the canonical splice acceptor site of intron 10, and RNA analysis shows this alters splicing and causes intron 10 retention leading to a premature termination codon; however the proportion of aberrant transcripts compared to wild type is unclear (Tao 2004). This variant is also reported in the ClinVar database (Variation ID: 41766) and is found in the East Asian population with an allele frequency of 1.5% (307/19952 alleles, including 5 homozygotes) in the Genome Aggregation Database, which is greater than expected for a pathogenic variant. Due to conflicting information, the clinical significance of the c.934-2A>G variant is uncertain at this time.

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.

The c.934-2A>G variant is predicted to lead to either nonsense-mediated mRNA decay or an abnormal protein product by destroying a canonical splice acceptor site. In vitro studies of this variant have demonstrated aberrant splicing and that the variant protein, if translated, is not localized to the nucleus (Tao 2004, Taki 2016). The c.934-2A>G variant was identified in 1.6% of East Asian chromosomes in the Genome Aggregation Database (http://gnomad.broadinstitute.org). This variant has been reported in the literature in a heterozygous state in multiple individuals with colorectal cancer; however has never, to our knowledge, been reported in an affected individual that is homozygous or compound heterozygous for a second MUTYH pathogenic variant (Miyaki 2005, Kim 2007, Taki 2016).

This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).

Converted during submission to Likely pathogenic.

The MUTYH c.934-2A>G variant was identified in 19 of 2400 proband chromosomes and 1 homozygous proband at a frequency of 0.025 from East Asian (Japanese, Chinese and Korean) individuals with colorectal polyps and/or colorectal, gastric and breast cancers and was present in 21 of 1206 control chromosomes (frequency: 0.014) from healthy individuals (Tao 2004, Lin 2016, Zhang 2017, Miyaki 2005, Jang 2015, Johnston 2012, Taki 2016 and Kim 2007). The variant was also identified in the following databases: dbSNP (ID: rs77542170 as “With other allele”) and ClinVar (1x as pathogenic by Soonchunhyang University Bucheon Hospital; 4x as likely pathogenic by Invitae, GeneDx, Quest Diagnostics, and Biesecker Lab/NIH; and 3x as uncertain significance by Ambry Genetics, Laboratory for Molecular Medicine, and Integrated Genetics/Laboratory Corporation of America). The variant was not identified in the Cosmic, MutDB or UMD-LSDB databases. The variant was identified in control databases in 298 of 277146 chromosomes (5 homozygous) at a frequency of 0.001 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: East Asian in 293 of 18870 chromosomes (5 homozygous, freq: 0.015), and South Asian in 5 of 30782 chromosomes (freq: 0.0002) and the variant was not observed in the African, Other, Latino, European Non-Finnish, Ashkenazi Jewish or Finnish populations. The c.934-2A>G variant is predicted to cause abnormal splicing because the nucleotide substitution occurs in the invariant region of the splice consensus sequence, and 4 of 4 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) predict a greater than 10% difference in splicing. Two independent studies have shown the MUTYH c.934-2A>G variant results in an aberrant mRNA transcript which retains intron 10, has a premature stop codon in exon 11, and encodes a truncated protein (Tao 2004 and Taki 2015). Further, in vitro expression studies demonstrate that, if translated, the variant protein is not localized in the nucleus like the wild type protein, suggesting insufficient ability of the variant protein to repair nuclear DNA (Tao 2004). In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more pathogenic role for this variant. This variant is classified as likely pathogenic.

This variant was determined to be likely pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has previously been reported as disease-causing [PMID 15180946, 22703879, 24733792, 24728327] With updated public general population genomic data and literatures, we now reclassified this variant as likely pathogenic [PMID 26332594, 26684149]