rs587777627
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_002691.4(POLD1):c.1421T>C(p.Leu474Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L474I) has been classified as Uncertain significance.
Frequency
Consequence
NM_002691.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
POLD1 | NM_002691.4 | c.1421T>C | p.Leu474Pro | missense_variant | 12/27 | ENST00000440232.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POLD1 | ENST00000440232.7 | c.1421T>C | p.Leu474Pro | missense_variant | 12/27 | 1 | NM_002691.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 36
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Colorectal cancer, susceptibility to, 10 Pathogenic:4Other:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Counsyl | Jun 10, 2016 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Nov 08, 2021 | - - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Apr 19, 2023 | This variant is considered likely pathogenic. This variant has been reported in multiple individuals with clinical features of gene-specific disease [PMID: 24501277, 26133394, 28306219]. This variant is expected to disrupt protein structure [Myriad internal data]. - |
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Aug 21, 2022 | For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 144003). This missense change has been observed in individual(s) with colorectal cancer, endometrial cancer, breast cancer and gastrointestinal stromal tumor (PMID: 24501277, 26133394, 28306219). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces leucine, which is neutral and non-polar, with proline, which is neutral and non-polar, at codon 474 of the POLD1 protein (p.Leu474Pro). - |
risk factor, no assertion criteria provided | literature only | OMIM | Jul 01, 2014 | - - |
Hereditary cancer-predisposing syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 27, 2021 | The p.L474P pathogenic mutation (also known as c.1421T>C), located in coding exon 11 of the POLD1 gene, results from a T to C substitution at nucleotide position 1421. The leucine at codon 474 is replaced by proline, an amino acid with similar properties. This variant is located within the highly conserved exonuclease domain of the POLD1 gene. This alteration was first reported in a female patient diagnosed with a colon cancer and a synchronous gastrointestinal stromal tumor (GIST) in the large bowel at age 36, whose family also met Amsterdam II criteria. Authors described this alteration as pathogenic, supported by cosegregation in the family, in silico predictions, previously published yeast assays, as well as the fact that this alteration's location is paralogous to the well described residue in POLE where the recurrent p.L424V mutation occurs (Valle L et al. Hum. Mol. Genet. 2014 Jul; 23(13):3506-12). The yeast based functional assay that the authors of Valle et al. describe was performed on the homologous residue (p.L479 Pol3) in yeast, and was shown to cause a mutator phenotype (Murphy K et al. Genome 2006 Apr; 49(4):403-10). This alteration has also been described in a woman with colorectal cancer and gastric polyps at age 23 as well as benign esophageal tumor at age 25. This alteration was also shown to segregate with disease in the family (Bellido F et al, Genet. Med. 2015 Jul;2). In addition, this alteration was identified in two Spanish families with colorectal cancer and breast cancer and is suggested to be a Spanish founder mutation. The tumor of one proband, which exhibited MSI and loss of MLH1 and PMS2 on IHC, had two MLH1 mutations. The authors posited that these somatic MLH1 mutations were a consequence of POLD1 inactivation (Ferrer-Avargues R et al. J Gene Med. 2017 Apr;19(4)). Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at