Total submissions: 4
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Ambry Genetics | RCV000564600 | SCV000674231 | likely pathogenic | Hereditary cancer-predisposing syndrome | 2024-09-11 | criteria provided, single submitter | clinical testing | The c.803+5G>A intronic variant results from a G to A substitution 5 nucleotides after coding exon 7 in the PMS2 gene. This alteration was identified as germline in conjunction with a pathogenic PMS2 somatic mutation in an individual with colorectal cancer that displayed high microsatellite instability (MSI-H) and loss of PMS2 on immunohistochemistry (IHC), but no MLH1 promoter hypermethylation was detected (Ambry internal data). Furthermore, in this family, c.803+5G>A segregated with disease in a sibling diagnosed with endometrial cancer that demonstrated loss of PMS2 on IHC (Ambry internal data). This alteration was also identified in two French patients, one with endometrial cancer that was MSI-H and the other with colorectal cancer that was MSI-H and also demonstrated loss of PMS2 on IHC (Wang Q et al. J Med Genet, 2020 07;57:487-499). This nucleotide position is well conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. RNA studies have demonstrated this alteration results in abnormal splicing in the set of samples tested (Ambry internal data). This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). Based on the majority of available evidence to date, this variant is likely to be pathogenic. |
| Labcorp Genetics |
RCV000630211 | SCV000751167 | likely pathogenic | Hereditary nonpolyposis colorectal neoplasms | 2025-01-08 | criteria provided, single submitter | clinical testing | This sequence change falls in intron 7 of the PMS2 gene. It does not directly change the encoded amino acid sequence of the PMS2 protein. It affects a nucleotide within the consensus splice site. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individuals with PMS2-related conditions (PMID: 31992580; external communication, internal data). ClinVar contains an entry for this variant (Variation ID: 486041). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Studies have shown that this variant is associated with altered splicing resulting in multiple RNA products (internal data). In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. |
| Laboratory for Molecular Medicine, |
RCV004017680 | SCV004848537 | likely pathogenic | Lynch syndrome | 2021-09-30 | criteria provided, single submitter | clinical testing | The c.803+5G>A variant in PMS2 has been reported in at least 5 individuals with lynch syndrome-associated cancers (Karam 2019 PMID:31642931, Wang 2020 PMID:31992580, Ambry data). In addition, tumors sampled from 2 of these individuals showed either high microsatellite instability or lacked PMS2 expression (Wang 2020 PMID:31992580). This variant has also been reported by other clinical laboratories in ClinVar (Variation ID 486041) and has also been identified in 0.001% (1/67946) of European chromosomes by gnomAD (http://gnomad.broadinstitute.org, gnomAD v3.1.1). This variant is located in the 5' splice region and computational tools predict an impact to splicing. In vitro studies on patient RNA have shown that this variant results in abnormal splicing (Karam 2019 PMID:31642931). In summary, although additional studies are required to fully establish its clinical significance, this variant meets criteria to be classified as likely pathogenic for autosomal dominant Lynch syndrome. ACMG/AMP Criteria applied: PS4_Moderate, PS3_Moderate, PM2_Supporting, PP3. |
| All of Us Research Program, |
RCV004017680 | SCV005429629 | likely pathogenic | Lynch syndrome | 2024-08-31 | criteria provided, single submitter | clinical testing | The c.803+5G>A variant in the PMS2 gene is located at the canonical splice site of intron 7 and is predicted to inflict donor loss (SpliceAI delta score: 0.98), resulting in alternative splicing and disrupted protein product. The variant has been reported in individuals with colorectal/endometrial/ovarian cancer (PMID: 31992580, 38311346). Patient peripheral blood RNA RT-PCR analysis demonstrated aberrant transcripts with either partial deletion or out-of-frame skipping of exon 7 (PMID: 38311346). Other splice variants located in the same splice junction (c.803+1G>T, c.803+1G>A) have also been reported from individuals with colorectal/endometrial cancer (PMID: 3501477, 36091691, 862267). Loss-of-function variants in the PMS2 gene are known to be pathogenic (PMID: 28514183, 25512458, 35223509). This variant has been reported in ClinVar (ID: 486041). This variant is absent in the general population according to gnomAD (v4.1). Therefore, the c.803+5G>A variant in the PMS2 gene is classified as likely pathogenic. |