POLD1 (DNA polymerase delta 1, catalytic subunit)

2018-05-01   Enric Domingo 

Identity

HGNC
LOCATION
19q13.33
LOCUSID
ALIAS
POLD

Abstract

Review on POLD1, with data on DNA, on the protein encoded, and where the gene is implicated.

DNA/RNA

Description

POLD1 gene is 33.7 kb long and composed of 1 non-coding exon followed by 25 coding exons and one last exon with both coding and 3 UTR regions.

Transcription

The length of the transcript is 3444 bp and results in a protein of 1107 residues.

Pseudogene

There is a pseudogene in chr 6q13 (LOC100422453).

Proteins

Description

The POLD1 gene encodes for p125 which is one of the four subunits that form Polδ (DNA polymerase delta) together with POLD2, POLD3 and POLD4 genes. This protein is one of the main DNA replicases in eukaryotes and is responsible of the replication of the lagging strand. POLD1 contains both the catalytic active site and the proofreading exonuclease domain (residues 245-571). Accordingly, the POLD1 gene confers to Polδ both replicative and 3 to 5 repair capabilities for the new strand.

Expression

Broadly expressed.

Localisation

Nuclear.

Function

Polδ is responsible of the polymerization of the lagging strand during DNA replication in yeast and humans. It also possesses 3 to 5 exonuclease capability to repair missincorporated nucleotides during DNA replication. Polδ is also involved in DNA repair pathways such as mismatch repair (MMR), base excision repair (BER), nucleotide excision repair (NER) or double-strand break repair.

Mutations

Germinal

A few missense germline mutations in the proofreading domain of POLD1 have been shown to be pathogenic such as D316G/H, P327L, R409W, L474P or S478N. These are extremely rare in the population and affect the exonuclease repair of Polδ hence resulting in a mutation rate increase of about 100-fold. Accordingly, these tumours are usually called ultramutated.

Somatic

Although some somatic mutations in POLD1 have been reported for different tumour types, most of them are very likely to be passengers. They are usually found either in non-hypermutated tumours or in hypermutated tumours due to mismatch repair deficiency. So far no POLD1 somatic mutation has clearly been shown to be pathogenic.

Implicated in

Entity name
Proofreading-associated polyposis (PPAP)
Disease
Autosomal dominant disease with high risk for endometrial carcinoma and/or colorectal adenoma or colorectal carcinoma due to germline mutations in POLE or POLD1 genes.
Prognosis
Probably good prognosis in early disease. Although not formally proven in POLD1 tumours, hypermutated tumours due to analog mutations in the polymerase gene POLE that shows a similar phenotype are highly immunogenic resulting in better prognosis. In addition, these patients are likely to respond to immune checkpoint inhibition.

Other Information

Locus ID:

NCBI: 5424
MIM: 174761
HGNC: 9175
Ensembl: ENSG00000062822

Variants:

dbSNP: 5424
ClinVar: 5424
TCGA: ENSG00000062822
COSMIC: POLD1

RNA/Proteins

Gene IDTranscript IDUniprot
ENSG00000062822ENST00000440232P28340
ENSG00000062822ENST00000440232A0A024R4F4
ENSG00000062822ENST00000593407M0QXE6
ENSG00000062822ENST00000593887M0R2J2
ENSG00000062822ENST00000593981M0QXQ2
ENSG00000062822ENST00000595904M0R2B7
ENSG00000062822ENST00000599857P28340
ENSG00000062822ENST00000599857A0A024R4F4
ENSG00000062822ENST00000600859M0QZR8
ENSG00000062822ENST00000601098P28340
ENSG00000062822ENST00000601098A0A024R4F4
ENSG00000062822ENST00000601098M0R2I8
ENSG00000062822ENST00000613923A0A087WYJ2
ENSG00000062822ENST00000643407A0A2R8Y7K6
ENSG00000062822ENST00000644560A0A2R8Y705

Expression (GTEx)

0
10
20
30
40
50
60

Pathways

PathwaySourceExternal ID
Purine metabolismKEGGko00230
Pyrimidine metabolismKEGGko00240
DNA replicationKEGGko03030
Base excision repairKEGGko03410
Nucleotide excision repairKEGGko03420
Mismatch repairKEGGko03430
Homologous recombinationKEGGko03440
Purine metabolismKEGGhsa00230
Pyrimidine metabolismKEGGhsa00240
DNA replicationKEGGhsa03030
Base excision repairKEGGhsa03410
Nucleotide excision repairKEGGhsa03420
Mismatch repairKEGGhsa03430
Homologous recombinationKEGGhsa03440
Metabolic pathwaysKEGGhsa01100
HTLV-I infectionKEGGko05166
HTLV-I infectionKEGGhsa05166
DNA polymerase delta complexKEGGhsa_M00262
DNA polymerase delta complexKEGGM00262
Cell CycleREACTOMER-HSA-1640170
Cell Cycle, MitoticREACTOMER-HSA-69278
S PhaseREACTOMER-HSA-69242
Synthesis of DNAREACTOMER-HSA-69239
DNA strand elongationREACTOMER-HSA-69190
Leading Strand SynthesisREACTOMER-HSA-69109
Polymerase switchingREACTOMER-HSA-69091
Lagging Strand SynthesisREACTOMER-HSA-69186
Processive synthesis on the lagging strandREACTOMER-HSA-69183
Removal of the Flap IntermediateREACTOMER-HSA-69166
Chromosome MaintenanceREACTOMER-HSA-73886
Telomere MaintenanceREACTOMER-HSA-157579
Extension of TelomeresREACTOMER-HSA-180786
Telomere C-strand (Lagging Strand) SynthesisREACTOMER-HSA-174417
Polymerase switching on the C-strand of the telomereREACTOMER-HSA-174411
Processive synthesis on the C-strand of the telomereREACTOMER-HSA-174414
Removal of the Flap Intermediate from the C-strandREACTOMER-HSA-174437
DNA ReplicationREACTOMER-HSA-69306
MetabolismREACTOMER-HSA-1430728
Cytosolic iron-sulfur cluster assemblyREACTOMER-HSA-2564830
DNA RepairREACTOMER-HSA-73894
Base Excision RepairREACTOMER-HSA-73884
Resolution of Abasic Sites (AP sites)REACTOMER-HSA-73933
Resolution of AP sites via the multiple-nucleotide patch replacement pathwayREACTOMER-HSA-110373
PCNA-Dependent Long Patch Base Excision RepairREACTOMER-HSA-5651801
DNA Damage BypassREACTOMER-HSA-73893
Recognition of DNA damage by PCNA-containing replication complexREACTOMER-HSA-110314
Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA templateREACTOMER-HSA-110313
Termination of translesion DNA synthesisREACTOMER-HSA-5656169
Mismatch RepairREACTOMER-HSA-5358508
Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)REACTOMER-HSA-5358565
Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)REACTOMER-HSA-5358606
DNA Double-Strand Break RepairREACTOMER-HSA-5693532
Homology Directed RepairREACTOMER-HSA-5693538
HDR through Homologous Recombination (HR) or Single Strand Annealing (SSA)REACTOMER-HSA-5693567
HDR through Homologous Recombination (HRR)REACTOMER-HSA-5685942
Nucleotide Excision RepairREACTOMER-HSA-5696398
Global Genome Nucleotide Excision Repair (GG-NER)REACTOMER-HSA-5696399
Dual Incision in GG-NERREACTOMER-HSA-5696400
Gap-filling DNA repair synthesis and ligation in GG-NERREACTOMER-HSA-5696397
Transcription-Coupled Nucleotide Excision Repair (TC-NER)REACTOMER-HSA-6781827
Dual incision in TC-NERREACTOMER-HSA-6782135
Gap-filling DNA repair synthesis and ligation in TC-NERREACTOMER-HSA-6782210

Protein levels (Protein atlas)

Not detected
Low
Medium
High

References

Pubmed IDYearTitleCitations
232634902013Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas.319
235285592013DNA polymerase ε and δ exonuclease domain mutations in endometrial cancer.105
199131212009Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.85
224659572012DNA polymerase δ and ζ switch by sharing accessory subunits of DNA polymerase δ.85
234474012013Germline and somatic polymerase ε and δ mutations define a new class of hypermutated colorectal and endometrial cancers.85
187014352008Polygenic model of DNA repair genetic polymorphisms in human breast cancer risk.63
245012772014New insights into POLE and POLD1 germline mutations in familial colorectal cancer and polyposis.53
261333942016POLE and POLD1 mutations in 529 kindred with familial colorectal cancer and/or polyposis: review of reported cases and recommendations for genetic testing and surveillance.48
237706082013An in-frame deletion at the polymerase active site of POLD1 causes a multisystem disorder with lipodystrophy.45
172033052007Genetic variation in the base excision repair pathway and bladder cancer risk.43

Citation

Enric Domingo

POLD1 (DNA polymerase delta 1, catalytic subunit)

Atlas Genet Cytogenet Oncol Haematol. 2018-05-01

Online version: http://atlasgeneticsoncology.org/gene/80665/pold1-(dna-polymerase-delta-1-catalytic-subunit)