NM_000535.7:c.703C>T
Variant summary
Our verdict is Pathogenic. Variant got 20 ACMG points: 20P and 0B. PVS1PM2PP3_ModeratePP5_Very_Strong
The NM_000535.7(PMS2):c.703C>T(p.Gln235*) variant causes a stop gained, splice region change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 3/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★). Synonymous variant affecting the same amino acid position (i.e. Q235Q) has been classified as Uncertain significance. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000535.7 stop_gained, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD4 exome Cov.: 33
GnomAD4 genome
ClinVar
Submissions by phenotype
Hereditary nonpolyposis colon cancer Pathogenic:1
Variant summary: PMS2 c.703C>T (p.Gln235X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory. In addition, as the variant alters a conserved nucleotide located in the putative exonic splice region close to the canonical splice donor site, several computational tools predict a significant impact on normal splicing: Four predict the variant abolishes the canonical 5' splicing donor site. However, these predictions have yet to be confirmed by functional studies. Either of these variant effects, namely truncation or splicing impact, will result in a loss of PMS2 function. The variant was absent in 251490 control chromosomes. c.703C>T has been reported in the literature in individuals affected with colorectal cancer and has also been reported as a pathogenic finding in at-least one individual undergoing population screening in the Healthy Nevada project (example, Truninger_2005, Espenschied_2017, Grzymski_2020). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014, although an expert panel (InSIGHT) and a clinical diagnostic laboratory have submitted clinical-significance assessments as pathogenic before 2014. Based on the evidence outlined above, the variant was classified as pathogenic. -
Lynch syndrome Pathogenic:1
Coding sequence variation resulting in a stop codon -
not provided Pathogenic:1
Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Observed in patients with Lynch-related cancers and tumor studies consistent with pathogenic variants in this gene (Truninger 2005); Not observed in large population cohorts (gnomAD); Truncating variants in this gene are considered pathogenic by a well-established clinical consortium and/or database; This variant is associated with the following publications: (PMID: 25525159, 32719484, 15887099) -
Hereditary nonpolyposis colorectal neoplasms Pathogenic:1
This sequence change creates a premature translational stop signal (p.Gln235*) in the PMS2 gene. RNA analysis indicates that this premature translational stop signal induces altered splicing and may result in an absent or altered protein product. This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with clinical features of Lynch syndrome (PMID: 15887099, 28514183). ClinVar contains an entry for this variant (Variation ID: 91363). Studies have shown that this premature translational stop signal results in activation of a cryptic splice site, and produces a non-functional protein and/or introduces a premature termination codon (Invitae). For these reasons, this variant has been classified as Pathogenic. -
Hereditary cancer-predisposing syndrome Pathogenic:1
The p.Q235* pathogenic mutation (also known as c.703C>T), located in coding exon 6 of the PMS2 gene, results from a C to T substitution at nucleotide position 703. This changes the amino acid from a glutamine to a stop codon within coding exon 6. This mutation was reported in a Swiss early-onset colorectal cancer patient whose tumor showed loss of expression of PMS2 on IHC and whose family history met Amsterdam criteria (Truninger K et al. Gastroenterology, 2005 May;128:1160-71). This variant has also been reported in 1/60,466 breast cancer cases and in 0/53,461 controls (Dorling et al. N Engl J Med. 2021 02;384:428-439). In addition to the clinical data presented in the literature, this alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. -
Lynch syndrome 4 Pathogenic:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at