ClinVar Miner

Submissions for variant NM_002691.4(POLD1):c.1186dup (p.Tyr396fs)

dbSNP: rs1414945254
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000657285 SCV000779016 uncertain significance not provided 2018-12-04 criteria provided, single submitter clinical testing This duplication of one nucleotide in POLD1 is denoted c.1186dupT at the cDNA level and p.Tyr396LeufsX239 (Y396LfsX239) at the protein level. The normal sequence, with the base that is duplicated in brackets, is CGGT[dupT]ACAA. The duplication causes a frameshift which changes a Tyrosine to a Leucine at codon 396, and creates a premature stop codon at position 239 of the new reading frame. Although this variant has not, to our knowledge, been reported in the literature, it is predicted to cause loss of normal protein function through either protein truncation or nonsense-mediated mRNA decay. However, while some missense variants in POLD1 have been recognized as an underlying cause of Polymerase Proofreading-Associated Polyposis (PPAP), there are no data at this time to support that loss-of-function variants confer the same cancer risks. We therefore consider this variant to be of uncertain significance with respect to cancer.
Invitae RCV001325245 SCV001516230 uncertain significance Colorectal cancer, susceptibility to, 10 2020-02-24 criteria provided, single submitter clinical testing Missense variants that disrupt the 3'-5' exonuclease (proof-reading) activity of the POLD1 protein, while not abolishing its polymerase enzyme activity, are associated with an increased risk for colonic adenomatous polyps and colon cancer (PMID: 23263490, 23447401). Loss-of-function variants, which result in an absent or severely disrupted POLD1 protein, are therefore unlikely to be associated with disease. Without further clinical and genetic evidence, however, this variant has been classified as a Variant of Uncertain Significance. This variant has not been reported in the literature in individuals with POLD1-related conditions. ClinVar contains an entry for this variant (Variation ID: 545761). This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Tyr396Leufs*239) in the POLD1 gene. It is expected to result in an absent or disrupted protein product.
Ambry Genetics RCV002331285 SCV002634095 uncertain significance Hereditary cancer-predisposing syndrome 2015-12-22 criteria provided, single submitter clinical testing The c.1186dupT variant, located in coding exon 9 of the POLD1 gene, results from a duplication of one nucleotide at position 1186, causing a translational frameshift with a predicted alternate stop codon. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6503 samples (13006 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.004% (greater than 25000 alleles tested) in our clinical cohort. As neither this specific alteration nor loss of function as a mechanism of pathogenicity have been well-described in the POLD1 gene, the clinical significance of this variant remains unknown (ACMG Standards and guidelines for the interpretation of sequence variants. Genet Med. 2015 May;17(5):405-23).

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