rs1060501335
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_001048174.2(MUTYH):āc.1079T>Cā(p.Leu360Pro) variant causes a missense change. The variant allele was found at a frequency of 0.00000205 in 1,461,720 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 (ā ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L360V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001048174.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MUTYH | NM_001128425.2 | c.1163T>C | p.Leu388Pro | missense_variant | 12/16 | ENST00000710952.2 | |
MUTYH | NM_001048174.2 | c.1079T>C | p.Leu360Pro | missense_variant | 12/16 | ENST00000456914.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MUTYH | ENST00000710952.2 | c.1163T>C | p.Leu388Pro | missense_variant | 12/16 | NM_001128425.2 | |||
MUTYH | ENST00000456914.7 | c.1079T>C | p.Leu360Pro | missense_variant | 12/16 | 1 | NM_001048174.2 | A1 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461720Hom.: 0 Cov.: 33 AF XY: 0.00000138 AC XY: 1AN XY: 727178
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Familial adenomatous polyposis 2 Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 28, 2024 | This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 388 of the MUTYH protein (p.Leu388Pro). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with adenomatous polyposis (PMID: 16134147, 16941501, 17949294). 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.1121 T>C, p.Leu374Pro, and p.L360P. ClinVar contains an entry for this variant (Variation ID: 406845). 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: 20848659, 23322991, 25820570). For these reasons, this variant has been classified as Pathogenic. - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 26, 2021 | Variant summary: MUTYH c.1163T>C (p.Leu388Pro) results in a non-conservative amino acid change located in the NUDIX hydrolase domain (IPR000086) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant was absent in 250094 control chromosomes (gnomAD and publications). c.1163T>C has been reported in the literature in compound heterozygous individuals affected with MUTYH-Associated Polyposis (e.g. Aceto_2005, Lejeune_2006). These data indicate that the variant is likely to be associated with disease. Experimental evidence demonstrated the variant severely impacts protein activity (e.g. Goto_2010, Shinmura_2012, Komine_2015). Three ClinVar submitters (evaluation after 2014) cite the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Jan 17, 2024 | - - |
Hereditary cancer-predisposing syndrome Pathogenic:3
Likely pathogenic, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Mar 27, 2020 | This missense variant replaces leucine with proline at codon 388 of the MUTYH protein. This variant is also known as p.Leu360Pro and p.Leu374Pro based on alternate transcripts. Computational prediction 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 impairs DNA glycosylase activity (PMID: 20848659) and ability to suppress spontaneous mutation (PMID: 23322991, 25820570). This variant has been reported in compound heterozygosity with known pathogenic mutations in multiple individuals affected with adenomatous polyposis (PMID: 16134147, 16941501, 26511139). This variant has not been identified 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 | Ambry Genetics | Apr 20, 2023 | The p.L388P pathogenic mutation (also known as c.1163T>C), located in coding exon 12 of the MUTYH gene, results from a T to C substitution at nucleotide position 1163. The leucine at codon 388 is replaced by proline, an amino acid with similar properties. This alteration has been identified in one individual with approximately 40 colorectal adenomas in conjunction with a pathogenic founder mutation in MUTYH; the authors report this patient had no detectable APC mutation and that family studies confirmed these MUTYH alterations to be in trans, but did not provide further details (Aceto G et al. Hum. Mutat. 2005 Oct; 26(4):394). This alteration has been identified in several other individuals with multiple polyps; however, phase was not determined and specific clinical information including polyp count was not provided (Lejeune S et al. Hum. Mutat. 2006 Oct; 27(10):1064; Olschwang S et al. Genet. Test. 2007; 11(3):315-20). This alteration has also been detected in conjunction with another pathogenic mutation in MUTYH by our laboratory, but phase is unknown (Ambry internal data). Various functional assays designed to measure base excision repair function have found this alteration to result in a severely deficient protein (Goto M et al. Hum. Mutat. 2010 Nov; 31(11):E1861-74; Shinmura K et al. World J. Gastroenterol. 2012 Dec; 18(47):6935-42; Komine K et al. Hum. Mutat. 2015 Jul; 36(7):704-11). Of note, this alteration is also designated as p.L360P and p.L374P in published literature. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
Pathogenic, criteria provided, single submitter | curation | Sema4, Sema4 | Jul 14, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at