Alternative titles; symbols
HGNC Approved Gene Symbol: POLD1
Cytogenetic location: 19q13.33 Genomic coordinates (GRCh38): 19:50,384,323-50,418,018 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 19q13.33 | {Colorectal cancer, susceptibility to, 10} | 612591 | Autosomal dominant | 3 |
| Mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome | 615381 | Autosomal dominant | 3 |
The POLD1 gene encodes the catalytic and proofreading subunit of DNA polymerase-delta, which is responsible for DNA synthesis of the lagging strand during DNA replication (summary by Palles et al., 2013 and Weedon et al., 2013).
The DNA polymerase-delta complex is involved in DNA replication and repair, and it consists of the proliferating cell nuclear antigen (PCNA; 176740), the multisubunit replication factor C (see 102579), and the 4-subunit polymerase complex: POLD1, POLD2 (600815), POLD3 (611415), and POLD4 (611525) (Liu and Warbrick, 2006).
Syvaoja et al. (1990) purified DNA polymerases alpha (312040), delta, and epsilon (174762) from the same HeLa cell extract. The results of their studies supported the premise that the alpha, delta, and epsilon polymerases are distinct enzymes. PCNA is the auxiliary protein (cofactor) for DNA polymerase delta. Syvaoja and Linn (1989) identified a form of DNA polymerase delta in HeLa cells that is insensitive to PCNA. Lee and Toomey (1987) isolated DNA polymerase delta from human placenta and presented evidence that both its polymerase and its exonuclease activities are associated with a single protein. Lee (1988) concluded that the multiple forms of placenta DNA polymerase delta are the result of proteolysis during isolation and that all derive from one protein.
Chung et al. (1991) cloned cDNA corresponding to the POLD gene and showed that the 3,443-bp sequence encodes a polypeptide of 1,107 amino acids. The enzyme is 94% identical to bovine DNA polymerase delta and contains the numerous highly conserved regions previously observed in the bovine and yeast enzymes. The human enzyme also contains 2 putative zinc finger domains in the C-terminal region of the molecule as well as a putative nuclear localization signal at the N-terminal end.
Yang et al. (1992) also cloned human POLD cDNA and demonstrated that it is 3.5 kb long and encodes a protein of 1,107 amino acids with a calculated molecular mass of 124 kD. Northern blot analysis demonstrated that the mRNA is 3.4 kb.
Weedon et al. (2013) found expression of the POLD1 gene across a panel of human tissues, with high levels of expression in heart and lung.
Nishida et al. (1988) showed that DNA repair synthesis in human fibroblasts requires DNA polymerase delta. Dresler et al. (1988) showed that repair synthesis late after ultraviolet irradiation, like repair synthesis at earlier stages, is mediated by this enzyme.
Kamath-Loeb et al. (2000) showed that WRN functionally interacts with DNA polymerase delta, which is required for DNA replication and DNA repair.
Lydeard et al. (2007) showed that in haploid budding yeast, Rad51 (179617)-dependent break-induced replication (BIR) induced by HO endonuclease requires the lagging strand DNA polymerase alpha-primase complex as well as polymerase delta to initiate new DNA synthesis. Polymerase epsilon is not required for the initial primer extension step of BIR but is required to complete 30 kb of new DNA synthesis. Initiation of BIR also requires the nonessential DNA polymerase delta subunit polymerase-32 primarily through its interaction with another polymerase delta subunit, polymerase-31. HO-induced gene conversion, in which both ends of a double-strand break engage in homologous recombination, does not require polymerase-32. Polymerase-32 is also required for the recovery of both Rad51-dependent and Rad51-independent survivors in yeast strains lacking telomerase. The results of Lydeard et al. (2007) strongly suggested that both types of telomere maintenance pathways occur by recombination-dependent DNA replication. Thus, polymerase-32, dispensable for replication and for gene conversion, is uniquely required for BIR; this finding provided an opening into understanding how DNA replication restart mechanisms operate in eukaryotes.
By PCR analysis of DNA from a panel of 24 human/hamster hybrid cells, Chung et al. (1991) mapped the POLD gene to chromosome 19. Yang et al. (1992) localized the POLD gene to chromosome 19 by Southern blotting of EcoRI-digested DNA from a panel of rodent/human cell hybrids. By in situ hybridization, Kemper et al. (1992) assigned the POLD1 gene to 19q13.3-q13.4.
Goldsby et al. (1998) mapped the Pold1 gene to mouse chromosome 7.
Chang et al. (1995) showed that the human POLD1 gene contains 27 exons spanning approximately 32 kb. The gene has a GC-rich promoter region and multiple transcription start sites. Zhao and Chang (1997) found that the core promoter of the POLD1 gene extends 328 bp upstream from the major transcription start site. Multiple elements in this region, including two 11-bp direct repeats, play an important role in POLD1 promoter activity. Zhao and Chang (1997) showed that SP1 (189906) and SP3 (601804) can activate the POLD1 promoter through the direct repeat sequences.
Susceptibility to Colorectal Cancer 10
In affected members of 2 large multigenerational families with susceptibility to colorectal cancer-10 (CRCS10; 612591), Palles et al. (2013) identified a heterozygous mutation in the POLD1 gene (S478N; 174761.0001) at a highly conserved residue in the exonuclease domain. The S489N mutation was also identified in a third affected family in the validation phase of the study. The phenotype was characterized by the development of multiple colorectal adenomas and carcinomas early in adult life. However, 7 mutation carriers also developed endometrial carcinoma, and 1 patient had 2 primary brain tumors. Tumor tissue from 2 of 6 mutation carriers showed additional somatic mutations, most commonly in the APC (611731), KRAS (190070), or FBXW7 (606278) genes. All tumors showed microsatellite stability. In addition to germline POLD1 mutations, Palles et al. (2013) identified somatic POLE (174762) mutations in 5 colorectal cancers from a large database. All of these tumors had additional somatic mutations. These findings suggested that the mechanism of tumorigenesis in POLD1-mutated tumors is decreased fidelity of replication-associated polymerase proofreading, leading to an increased mutation rate.
Bellido et al. (2016) sequenced the exonuclease domains of POLE and POLD1 in 529 kindreds, 441 with familial nonpolyposis CRC and 88 with polyposis. They identified 7 novel or rare variants. In addition to the POLE L424V recurrent mutation in a patient with polyposis, CRC, and oligodendroglioma, Bellido et al. (2016) identified 6 novel or rare POLD1 variants in nonpolyposis CRC families.
Mandibular Hypoplasia, Deafness, Progeroid Features, and Lipodystrophy Syndrome
In 4 unrelated patients with mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome (MDPL; 615381), Weedon et al. (2013) identified a de novo heterozygous in-frame deletion of residue ser605 (ser604del) in the polymerase active site of the POLD1 gene (174761.0003). The mutation, which was initially found by exome sequencing and confirmed by Sanger sequencing in 2 of the patients, was not found in any of the parents or in several large control databases. The disorder was characterized by loss of subcutaneous fat in early childhood, a characteristic facial appearance, and metabolic abnormalities including insulin resistance and diabetes mellitus. Sensorineural deafness occurred late in the first or second decades of life. In vitro functional expression studies in E. coli showed that the mutant enzyme had lost its DNA polymerase ability, whereas its exonuclease activity, although decreased compared to wildtype, was still present. The studies demonstrated decoupling of the mutant enzyme's activities and suggested that the mutant protein could bind DNA, but was unable to interact with and incorporate dNTPs. The mutations causing colorectal cancer (174761.0001 and 174761.0002) affect the proofreading domain and lead to increased base-substitution error rates, whereas the ser605del mutant enzyme retains proofreading ability but cannot catalyze polymerization, which likely leads to an increase in stalled replication forks, cell senescence, and death. The findings implicated POLD1 in adipose tissue homeostasis.
Associations Pending Confirmation
For discussion of a possible association between a syndromic combined immunodeficiency disorder and variation in the POLD1 gene, see 174761.0005.
Normal cells minimize spontaneous mutations through the combined actions of polymerase base selectivity, 3-prime to 5-prime exonucleolytic proofreading, mismatch correction, and DNA damage repair. To determine the consequences of defective proofreading in mammals, Goldsby et al. (2002) generated mice with a point mutation (asp400 to ala) in the proofreading domain of DNA polymerase delta. They showed that this mutation inactivates the 3-prime to 5-prime exonuclease of DNA polymerase delta and causes a mutator and cancer phenotype in a recessive manner. By 18 months of age, 94% of mice homozygous for the mutation developed cancer and died (median survival, 10 months). In contrast, only 3 to 4% of heterozygotes and wildtype homozygotes developed cancer in this time frame. Of the 66 tumors arising in 49 homozygous mice, 40 were epithelial in origin (carcinomas), 24 were mesenchymal (lymphomas and sarcomas), and 2 were composite (teratomas); one-third of these animals developed tumors in more than 1 tissue. Skin squamous cell carcinoma was the most common tumor type, occurring in 60% of all homozygous mice and in 90% of those surviving beyond 8 months of age. These data showed that DNA polymerase delta proofreading suppresses spontaneous tumor development and strongly suggested that unrepaired DNA polymerase errors contribute to carcinogenesis.
In affected members of 2 large multigenerational families with susceptibility to colorectal cancer-10 (CRCS10; 612591), Palles et al. (2013) identified a heterozygous c.1433G-A transition (c.1433G-A, NM_002691) in the POLD1 gene, resulting in a ser478-to-asn (S478N) substitution at a highly conserved residue in the exonuclease domain. The mutant mRNA was stably expressed. Microsatellite analysis of the 2 families suggested a common ancestor. The S489N mutation was identified in a third affected family in the validation phase of the study. The mutation, which was initially identified by linkage analysis combined with whole-genome sequencing, was not found in 6,721 controls or 10,755 control exomes. A yeast construct carrying the analogous mutation showed a 12-fold higher mutation rate compared to wildtype. Molecular modeling using yeast structures indicated that the S478N mutation will distort the packing of helices involved at the exonuclease active site, likely affecting nuclear activity. The phenotype was characterized by the development of multiple colorectal adenomas and carcinomas early in adult life. However, 7 mutation carriers also developed endometrial carcinoma, and 1 patient had 2 primary brain tumors. Tumor tissue from 2 of 6 mutation carriers showed additional somatic mutations, most commonly in the APC (611731), KRAS (190070), or FBXW7 (606278) genes. All tumors showed microsatellite stability.
Elsayed et al. (2015) did not identify the POLD1 S478N mutation in 1,188 Dutch probands with multiple polyps or familial colorectal cancer.
In a 70-year-old patient with multiple colorectal adenomas (612591), Palles et al. (2013) identified a heterozygous c.981C-G transversion (c.981C-G, NM_002691) in the POLD1 gene, resulting in a pro327-to-leu (P327L) substitution at a highly conserved residue in the exonuclease domain.
In 4 unrelated patients with mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome (MDPL; 615381), Weedon et al. (2013) identified a de novo heterozygous in-frame 3-bp deletion (c.1812_1814delCTC, NM_002691.2) in the POLD1 gene, resulting in the deletion of residue ser605 (ser605del) in motif A, a highly conserved region of the polymerase active site. The mutation, which was initially found by exome sequencing and confirmed by Sanger sequencing in 2 of the patients, was not found in any of the parents or in several large control databases. In vitro functional expression studies in E. coli showed that the mutant enzyme had lost its DNA polymerase ability, whereas its exonuclease activity, although decreased compared to wildtype, was still present. These studies demonstrated decoupling of the mutant enzyme's activities and suggested that the mutant protein could bind DNA, but was unable to interact with and incorporate dNTPs. The findings implicated POLD1 in adipose tissue homeostasis.
In a woman with CRCS10 (612591) without polyposis, Valle et al. (2014) identified a heterozygous c.1421T-C transition (c.1421T-C, NM_002691) in the POLD1 gene, resulting in a leu474-to-pro (L474P) substitution at a highly conserved residue in the DNA proofreading domain. The mutation was also present in the patient's maternal aunt, who had colorectal cancer and endometrial cancer, as well as in the patient's mother, who had endometrial cancer. There were no defects in mismatch repair in this family. A mutation at the homologous codon in yeast (L479S) has been shown to cause a mutator phenotype (Murphy et al., 2006), supporting the pathogenicity of the L474P mutation. The proband was ascertained from a cohort of 858 Spanish probands with familial/early-onset CRC who underwent screening of the POLD1 gene, thus accounting for 0.12% of the total.
This variant is classified as a variant of unknown significance because its contribution to a syndromic combined immunodeficiency disorder has not been confirmed.
In a 24-year-old man (patient 2) with a syndromic combined immunodeficiency disorder, Conde et al. (2019) identified 3 heterozygous missense variants in the POLD1 gene: a gln684-to-his (Q684H) substitution in the catalytic domain and a ser939-to-trp (S939W) substitution in an interdomain region that were inherited in cis from the mother, and an arg1074-to-trp (R1074W) in the CysB domain that was inherited from the father on the other allele. The Q684H and R1074W variants were present at low frequencies (less that 0.001%) in the heterozygous state only in the ExAC database, whereas S939W was absent from both ExAC and the 1000 Genomes Project database. Peripheral blood mononuclear cells from the patient showed decreased expression of other POLD components, suggesting impaired stability of the polymerase-delta complex, as well as decreased levels of cells active in the cell cycle. In vitro studies of HEK293 cells transfected with the variants showed that the stability of the POLD1 variant proteins was preserved. The POLD1 variants retained binding to other POLD subunits; however, the POLD1 variants resulted in reduced enzymatic polymerase activity compared to wildtype. The patient presented in early childhood with recurrent respiratory infections leading to bronchiectasis and skin warts that were negative for common papilloma virus strains. He had short stature, microcephaly, hearing impairment, and impaired intellectual development with an IQ of 70. Immunologic workup showed persistently decreased numbers of CD4+ T cells, B cells, and NK cells.
This variant is classified as a variant of unknown significance because its contribution to a syndromic combined immunodeficiency disorder has not been confirmed.
For discussion of the arg1074-to-trp (R1074W) substitution in the POLD1 gene that was found in compound heterozygous state in a patient with a syndromic combined immunodeficiency disorder by Conde et al. (2019), see 174761.0005.
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