ClinVar Genomic variation as it relates to human health

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Observed in individuals with MSH2-related cancers; tumor IHC analyses did not consistently show loss of MSH2 protein (Sun et al., 2004; Chao et al., 2019; Tian et al., 2019); Published functional studies are conflicting: showed defective RNA and protein expression as well as cell viability and response to DNA-damaging agents in one study (Arora et al., 2017) and normal mismatch repair function and cell growth rates in another (Jia et al., 2020); This variant is associated with the following publications: (PMID: 14514376, 29192238, 15046089, 16425354, 18383312, 26333163, 26845104, 28580595, 29050249, 28706299, 31386297, 32255556, 32566746, 30798936, 35538921, 31569399, 18822302, 21120944, 30982232, 33357406, 33471991, 33309985, 32019277, 23760103, 31307542, 35057767, 33294277, 30374176, 31054147, 28494185)

This missense variant replaces proline with glutamine at codon 5 of the MSH2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). An RNA study reported no splicing defect detected in carrier RNA (PMID: 16425354; InSiGHT database). However, a functional study reported that this variant showed RNA expression defect in transfected cell lines (PMID: 28494185). This variant has intermediate MSH2 function in a 6-thioguanine sensitivity assay in haploid human cells (internally defined LOF score threshold -1.32 < LOF score < 0.88, PMID: 33357406). This variant has been reported in individuals affected with colorectal, endometrial and gastric cancer (PMID: 14514376, 23760103, 26845104, 29050249, 31054147, 31307542, 33294277, 33309985), breast and ovarian cancer (PMID: 28580595, 30982232, 32019277, 32068069), pancreatic cancer (PMID: 32980694), and cancer unaffected controls (PMID: 32980694, 33309985). This variant has been identified in 8/251846 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

Internal laboratory data reveals that this variant has been detected in several individuals whose personal histories, family histories, or tumor profiles were not consistent with Lynch syndrome (internal data, unpublished).

Variant summary: MSH2 c.14C>A (p.Pro5Gln) results in a non-conservative amino acid change in the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3.2e-05 in 220468 control chromosomes. The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance.c.14C>A has been reported in the literature as a VUS in settings of multigene panel testing of individuals affected with a variety of cancers such as stomach/gastric, breast, Lynch tumors (example, Wang_2005, Shirts_2015, Kim_2017, Xie_2018, Chao_2019, Kiyozumi_2019, Tian_2019, Tsai_2019, Wang_2019, Kim_2022). Some of these reports included individuals with conflicting immunohistochemistry (IHC) findings such as normal IHC (example, Shirts_2015), stable MSI and normal IHC (example, Chao_2019) and at-least one report of an individual with colorectal cancer and negative staining for MSH2 but positive staining for MLH1, MSH6 and PMS2 (example, Tian_2019). These reports do not provide unequivocal conclusions about association of the variant with Hereditary Nonpolyposis Colorectal Cancer. Co-occurrences with other pathogenic variant(s) have been reported (MSH6 c.3261dupC, p.Phe1088fs, Kim_2022), providing supporting evidence for a benign role. At least one publication reports experimental evidence evaluating an impact on protein function, indicating that cells expressing the variant had nondetectable levels of MSH2 RNA and protein expression and impaired DNA-damage response in-vitro (Arora_2017). The following publications have been ascertained in the context of this evaluation (PMID: 26845104, 16425354, 28494185, 29050249, 28580595, 30374176, 30982232, 31307542, 31386297, 31054147, 35884469). Twelve submitters have cited clinical-significance assessments for this variant to ClinVar after 2014 and classified as likely benign (n=5) and VUS (n=7). Based on the evidence outlined above, the variant was classified as uncertain significance.

This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 27363726].

This missense variant replaces proline with glutamine at codon 5 of the MSH2 protein. Computational prediction suggests that this variant may have deleterious impact on protein structure and function (internally defined REVEL score threshold >= 0.7, PMID: 27666373). An RNA study reported no splicing defect detected in carrier RNA (PMID: 16425354; InSiGHT database). However, a functional study reported that this variant showed RNA expression defect in transfected cell lines (PMID: 28494185). This variant has intermediate MSH2 function in a 6-thioguanine sensitivity assay in haploid human cells (internally defined LOF score threshold -1.32 < LOF score < 0.88, PMID: 33357406). This variant has been reported in individuals affected with colorectal, endometrial and gastric cancer (PMID: 14514376, 23760103, 26845104, 29050249, 31054147, 31307542, 33294277, 33309985), breast and ovarian cancer (PMID: 28580595, 30982232, 32019277, 32068069), pancreatic cancer (PMID: 32980694), and cancer unaffected controls (PMID: 32980694, 33309985). This variant has been identified in 8/251846 chromosomes in the general population by the Genome Aggregation Database (gnomAD). The available evidence is insufficient to determine the role of this variant in disease conclusively. Therefore, this variant is classified as a Variant of Uncertain Significance.

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.

The MSH2 p.Pro5Gln variant was identified in 2 of 3138 proband chromosomes (freq: 0.001) from individuals with gastric cancer and was present in 3 of 4098 control chromosomes (freq: 0.001) from healthy Japanese individuals (Shirts 2016, Kim 2017, Yamaguchi-Kabata 2018). The variant was also identified in the following databases: dbSNP (rs56170584) as “With Uncertain significance allele”, ClinVar (classified as uncertain significance by Invitae, Ambry Genetics, GeneDx, Counsyl and three other submitters). The variant was not identified in the UMD LSDB database. The variant was identified in control databases in 7 of 214510 chromosomes at a frequency of 0.00003 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the East Asian population in 7 of 15668 chromosomes (freq: 0.0004) while the variant was not observed in the African, Other, Latino, European, Ashkenazi Jewish, Finnish or South Asian populations. The p.Pro5Gln residue is conserved in mammals but not in more distantly related organisms and 4 of 5 computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. This variant was identidied in one individual with gastric cancer and first-degree relatives with melanoma and breast cancer, although the proband demonstrated normal IHC and MMR levels (Kim 2017). One study showed greatly reduced mRNA and protein levels for this variant, possibly due to a predicted circular loop RNA structure (Arora 2017). In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

The MSH2 p.Pro5Gln variant was identified in 2 of 3138 proband chromosomes (freq: 0.001) from individuals with gastric cancer and was present in 3 of 4098 control chromosomes (freq: 0.001) from healthy Japanese individuals (Shirts 2016, Kim 2017, Yamaguchi-Kabata 2018). The variant was also identified in the following databases: dbSNP (rs56170584) as “With Uncertain significance allele”, ClinVar (classified as uncertain significance by Invitae, Ambry Genetics, GeneDx, Counsyl and three other submitters). The variant was not identified in the UMD LSDB database. The variant was identified in control databases in 7 of 214510 chromosomes at a frequency of 0.00003 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the East Asian population in 7 of 15668 chromosomes (freq: 0.0004) while the variant was not observed in the African, Other, Latino, European, Ashkenazi Jewish, Finnish or South Asian populations. The p.Pro5Gln residue is conserved in mammals but not in more distantly related organisms and 4 of 5 computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. This variant was identidied in one individual with gastric cancer and first-degree relatives with melanoma and breast cancer, although the proband demonstrated normal IHC and MMR levels (Kim 2017). One study showed greatly reduced mRNA and protein levels for this variant, possibly due to a predicted circular loop RNA structure (Arora 2017). In summary, based on the above information, the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.