ClinVar Genomic variation as it relates to human health

The POLD1 c.961G>A (p.Gly321Ser) missense change has a maximum subpopulation frequency of 0.066% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/variant/19-50905989-G-A). In silico tools are not in agreement about the effect of this variant on protein function, but to our knowledge these predictions have not been confirmed by functional assays. This variant has been reported in the literature in individuals with a personal and/or family history of colorectal cancer (PS4_supporting; PMID: 26648449, 30827058, 33193653), in an individual with colon polyps (PMID: 25938944), in an individual with multiple endocrine neoplasia, type II (PMID: 30680046), and in non-cancer controls (PMID: 30267214). One individual with >100 colorectal polyps and colorectal cancer diagnosed at age 37 also carried a heterozygous pathogenic variant in MUTYH (PMID: 30827058). In summary, this variant meets criteria to be classified as of uncertain significance based on the ACMG/AMP criteria: PS4_supporting.

This variant is classified as a variant of uncertain significance as there is insufficient evidence to determine its impact on protein function and/or cancer risk.

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.

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 30827058, 30680046, 20951805, 25938944, 27320729, 26648449, 28188185, 29120461, 33193653, 33332384, 34326862, 35264596, 37088804)

The POLD1 c.961G>A (p.Gly321Ser) variant has been reported in the published literature in individuals with colorectal polyps and colorectal cancer (PMIDs: 33193653 (2020), 30827058 (2019), 26648449 (2015), 25938944 (2015)). Functional studies demonstrated that this variant was damaging to protein function (PMID: 26648449 (2015)). The frequency of this variant in the general population, 0.00097 (25/25792 chromosomes in Swedish subpopulation (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is higher than would generally be expected for pathogenic variants in this gene. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is damaging. Based on the available information, we are unable to determine the clinical significance of this variant.

The POLD1 c.961G>A variant is predicted to result in the amino acid substitution p.Gly321Ser. This variant has been reported in an individual with adenomatous polyps and a family history of colorectal cancer or adenomatous polyposis (Weren et al. 2015. PubMed ID: 25938944) and an individual suspected of having Lynch syndrome (Jansen et al. 2016. PubMed ID: 26648449). It was also reported as a variant of uncertain significance in a study of individuals with early-onset colorectal cancer or familial colorectal cancer (Djursby et al. 2020. PubMed ID: 33193653) and in a study of patients with a suspected hereditary tumor syndrome (Henn et al. 2019. PubMed ID: 30680046). Two additional unrelated patients with multiple colorectal polyps and colorectal cancer were also reported to have this variant; however, the variant did not co-segregate with disease in one family and co-segregation analysis was unavailable for the other family (Table 2 and Figure 1A, Elsayed et al. 2019. PubMed ID: 30827058). This variant is reported in 0.066% of alleles in individuals of European (Non-Finnish) descent in gnomAD and has been interpreted as a variant of uncertain significance and likely benign in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/221136/). Although we suspect that this variant may be benign, at this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

The POLD1 p.Gly321Ser variant was identified in 5 of 1364 proband chromosomes (frequency: 0.004) from individuals with colorectal and medullary thyroid cancer (Weren 2015, Jansen 2016, Elsayed 2019, Henn 2019). The variant was identified in dbSNP (rs41554817) as “with uncertain significance allele”, ClinVar (interpreted as uncertain significance by Invitae, Ambry Genetics and 7 others). The variant was identified in control databases in 88 of 268,044 chromosomes at a frequency of 0.000328 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 3 of 23418 chromosomes (freq: 0.0001), Other in 1 of 6224 chromosomes (freq: 0.0002), Latino in 7 of 33,760 chromosomes (freq: 0.0002), European in 75 of 122,102 chromosomes (freq: 0.0006), Finnish in 1 of 24,360 chromosomes (freq: 0.00004), and South Asian in 1 of 29,884 chromosomes (freq: 0.00003). The variant was not observed in the Ashkenazi Jewish and East Asian populations. The variant affects the exonuclease domain of POLD1, but functional analysis would be needed to determine if there is a deleterious effect on the protein. The p.Gly321 residue is conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of 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. 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