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POLD1 DNA polymerase delta 1, catalytic subunit [ Homo sapiens (human) ]

Gene ID: 5424, updated on 7-Apr-2024

Summary

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Official Symbol
POLD1provided by HGNC
Official Full Name
DNA polymerase delta 1, catalytic subunitprovided by HGNC
Primary source
HGNC:HGNC:9175
See related
Ensembl:ENSG00000062822 MIM:174761; AllianceGenome:HGNC:9175
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CDC2; MDPL; POLD; CRCS10
Summary
This gene encodes the 125-kDa catalytic subunit of DNA polymerase delta. DNA polymerase delta possesses both polymerase and 3' to 5' exonuclease activity and plays a critical role in DNA replication and repair. Alternatively spliced transcript variants have been observed for this gene, and a pseudogene of this gene is located on the long arm of chromosome 6. [provided by RefSeq, Mar 2012]
Expression
Broad expression in bone marrow (RPKM 7.5), testis (RPKM 4.7) and 24 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
19q13.33
Exon count:
31
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 19 NC_000019.10 (50384323..50418018)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 19 NC_060943.1 (53471875..53505574)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (50887580..50921275)

Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105372437 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14983 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14984 Neighboring gene napsin A aspartic peptidase Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50879623-50880434 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10959 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10960 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10961 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50888337-50888838 Neighboring gene nuclear receptor subfamily 1 group H member 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50918101-50918885 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50918886-50919670 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10965 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10966 Neighboring gene ReSE screen-validated silencer GRCh37_chr19:50921334-50921502 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 14987 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50930914-50931487 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50931488-50932060 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10967 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 10968 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr19:50935955-50936713 Neighboring gene Spi-B transcription factor Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50937528-50938028 Neighboring gene myosin binding protein C2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr19:50954383-50954951

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. DNA Polymerase Delta Exhibits Altered Catalytic Properties on Lysine Acetylation. Njeri C, et al. Genes (Basel), 2023 Mar 23. PMID 37107532, Free PMC Article
  2. Scrutinizing Deleterious Nonsynonymous SNPs and Their Effect on Human POLD1 Gene. Bappy MNI, et al. Genet Res (Camb), 2022. PMID 35620275, Free PMC Article
  3. DNA Polymerase Delta 1 Catalytic Subunit (POLD1) as a Prognostic Factor in Clear Cell Renal Cell Carcinoma Patients. Godlewski J, et al. In Vivo, 2022 May-Jun. PMID 35478106, Free PMC Article
  4. A novel POLD1 pathogenic variant identified in two families with a cancer spectrum mimicking Lynch syndrome. Legrand C, et al. Eur J Med Genet, 2022 Feb. PMID 34954152
  5. DNA polymerase delta Exo domain stabilizes mononucleotide microsatellites in human cells. Shioi S, et al. DNA Repair (Amst), 2021 Dec. PMID 34530183

See all (231) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Rare germline variants in POLE and POLD1 encoding the catalytic subunits of DNA polymerases epsilon and delta in glioma families.
    Title: Rare germline variants in POLE and POLD1 encoding the catalytic subunits of DNA polymerases ε and δ in glioma families.
  2. POLD1 Is Required for Cell Cycle Progression by Overcoming DNA Damage in Malignant Pleural Mesothelioma.
    Title: POLD1 Is Required for Cell Cycle Progression by Overcoming DNA Damage in Malignant Pleural Mesothelioma.
  3. Race, Prevalence of POLE and POLD1 Alterations, and Survival Among Patients With Endometrial Cancer.
    Title: Race, Prevalence of POLE and POLD1 Alterations, and Survival Among Patients With Endometrial Cancer.
  4. DNA polymerase POLD1 promotes proliferation and metastasis of bladder cancer by stabilizing MYC.
    Title: DNA polymerase POLD1 promotes proliferation and metastasis of bladder cancer by stabilizing MYC.
  5. DNA Polymerase Delta Exhibits Altered Catalytic Properties on Lysine Acetylation.
    Title: DNA Polymerase Delta Exhibits Altered Catalytic Properties on Lysine Acetylation.
  6. Functional landscapes of POLE and POLD1 mutations in checkpoint blockade-dependent antitumor immunity.
    Title: Functional landscapes of POLE and POLD1 mutations in checkpoint blockade-dependent antitumor immunity.
  7. POLE/POLD1 mutation and tumor immunotherapy.
    Title: POLE/POLD1 mutation and tumor immunotherapy.
  8. Scrutinizing Deleterious Nonsynonymous SNPs and Their Effect on Human POLD1 Gene.
    Title: Scrutinizing Deleterious Nonsynonymous SNPs and Their Effect on Human POLD1 Gene.
  9. DNA Polymerase Delta 1 Catalytic Subunit (POLD1) as a Prognostic Factor in Clear Cell Renal Cell Carcinoma Patients.
    Title: DNA Polymerase Delta 1 Catalytic Subunit (POLD1) as a Prognostic Factor in Clear Cell Renal Cell Carcinoma Patients.
  10. Solving the enigma of POLD1 p.V295M as a potential cause of increased cancer risk.
    Title: Solving the enigma of POLD1 p.V295M as a potential cause of increased cancer risk.
Submit: New GeneRIF Correction See all GeneRIFs (81)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Colorectal cancer, susceptibility to, 10
MedGen: C2675481 OMIM: 612591 GeneReviews: Not available
Compare labs
Mandibular hypoplasia-deafness-progeroid syndrome
MedGen: C3715192 OMIM: 615381 GeneReviews: Not available
Compare labs

Copy number response

Description
Copy number response
Triplosensitivity

No evidence available (Last evaluated 2020-06-05)

ClinGen Genome Curation Page
Haploinsufficency

Little evidence for dosage pathogenicity (Last evaluated 2020-06-05)

ClinGen Genome Curation Page

EBI GWAS Catalog

Description
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3'-5'-DNA exonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables 4 iron, 4 sulfur cluster binding IEA
Inferred from Electronic Annotation
more info
  
enables DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables DNA-directed DNA polymerase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables DNA-directed DNA polymerase activity IMP
Inferred from Mutant Phenotype
more info
 PubMed 
enables chromatin binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables damaged DNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables enzyme binding IEA
Inferred from Electronic Annotation
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA biosynthetic process IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA repair TAS
Traceable Author Statement
more info
 PubMed 
involved_in DNA replication IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in DNA replication proofreading IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in DNA synthesis involved in DNA repair IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in DNA synthesis involved in DNA repair IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in DNA-templated DNA replication IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in DNA-templated DNA replication IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in base-excision repair, gap-filling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in base-excision repair, gap-filling IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in cellular response to UV IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in error-free translesion synthesis IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in fatty acid homeostasis IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nucleotide-excision repair, DNA gap filling IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nucleotide-excision repair, DNA gap filling IC
Inferred by Curator
more info
 PubMed 
involved_in nucleotide-excision repair, DNA gap filling IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in response to UV TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in aggresome IDA
Inferred from Direct Assay
more info
  
colocalizes_with chromosome, telomeric region IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol IDA
Inferred from Direct Assay
more info
  
part_of delta DNA polymerase complex IBA
Inferred from Biological aspect of Ancestor
more info
  
part_of delta DNA polymerase complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of delta DNA polymerase complex IPI
Inferred from Physical Interaction
more info
 PubMed 
located_in membrane HDA PubMed 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of nucleotide-excision repair complex IDA
Inferred from Direct Assay
more info
 PubMed 
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
DNA polymerase delta catalytic subunit
Names
3'-5' exodeoxyribonuclease
CDC2 homolog
DNA polymerase subunit delta p125
polymerase (DNA directed), delta 1, catalytic subunit 125kDa
polymerase (DNA) delta 1, catalytic subunit
NP_001243778.1
NP_001295561.1
NP_002682.2
XP_005259065.1
XP_011525340.1
XP_016882371.1
XP_047294902.1
XP_047294903.1
XP_047294904.1
XP_047294905.1
XP_047294906.1
XP_054177207.1
XP_054177208.1
XP_054177209.1
XP_054177210.1
XP_054177211.1
XP_054177212.1
XP_054177213.1
XP_054177214.1

NCBI Reference Sequences (RefSeq)

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NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_033800.1 RefSeqGene

    Range
    5001..38696
    Download
    GenBank, FASTA, Sequence Viewer (Graphics), LRG_785

mRNA and Protein(s)

  1. NM_001256849.1 → NP_001243778.1  DNA polymerase delta catalytic subunit isoform 1

    See identical proteins and their annotated locations for NP_001243778.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) contains an alternate exon in the 5' UTR and uses an alternate splice site in the 3' coding region, compared to variant 4. The encoded isoform (1) is shorter than isoform 2.
    Source sequence(s)
    AA236879, BC008800, CD101690
    Consensus CDS
    CCDS12795.1
    UniProtKB/Swiss-Prot
    P28340, Q8NER3, Q96H98
    UniProtKB/TrEMBL
    Q308M6
    Related
    ENSP00000473052.1, ENST00000599857.7
    Conserved Domains (1) summary
    PTZ00166
    Location:81 → 1100
    PTZ00166; DNA polymerase delta catalytic subunit; Provisional

  2. NM_001308632.1 → NP_001295561.1  DNA polymerase delta catalytic subunit isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) encodes the longer isoform (2).
    Source sequence(s)
    AC008655, AC020909, DQ234348
    Consensus CDS
    CCDS82381.1
    UniProtKB/TrEMBL
    M0R2B7, Q308M6
    Related
    ENSP00000472445.1, ENST00000595904.6
    Conserved Domains (4) summary
    cd05777
    Location:304 → 533
    DNA_polB_delta_exo; DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase
    cd05533
    Location:579 → 1000
    POLBc_delta; DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding ...
    PTZ00166
    Location:81 → 1126
    PTZ00166; DNA polymerase delta catalytic subunit; Provisional
    pfam14260
    Location:1038 → 1108
    zf-C4pol; C4-type zinc-finger of DNA polymerase delta

  3. NM_002691.4 → NP_002682.2  DNA polymerase delta catalytic subunit isoform 1

    See identical proteins and their annotated locations for NP_002682.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) contains an alternate exon in the 5' UTR and uses an alternate splice site in the 3' coding region, compared to variant 4. The encoded isoform (1) is shorter than isoform 2.
    Source sequence(s)
    AB209560, CD101690, M81735
    Consensus CDS
    CCDS12795.1
    UniProtKB/Swiss-Prot
    P28340, Q8NER3, Q96H98
    UniProtKB/TrEMBL
    Q308M6
    Related
    ENSP00000406046.1, ENST00000440232.7
    Conserved Domains (1) summary
    PTZ00166
    Location:81 → 1100
    PTZ00166; DNA polymerase delta catalytic subunit; Provisional

RNA

  1. NR_046402.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains an alternate first exon and lacks an internal exon in the 3' region, compared to variant 4. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 4, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AA236879, AB209560, CD101690
    Related
    ENST00000600859.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p14 Primary Assembly

    Range
    50384323..50418018
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047438947.1 → XP_047294903.1  DNA polymerase delta catalytic subunit isoform X1

    UniProtKB/Swiss-Prot
    P28340, Q8NER3, Q96H98

  2. XM_047438949.1 → XP_047294905.1  DNA polymerase delta catalytic subunit isoform X2

    UniProtKB/TrEMBL
    A0A087WYJ2

  3. XM_047438946.1 → XP_047294902.1  DNA polymerase delta catalytic subunit isoform X1

    UniProtKB/Swiss-Prot
    P28340, Q8NER3, Q96H98
    Related
    ENSP00000510052.1, ENST00000687454.1

  4. XM_047438948.1 → XP_047294904.1  DNA polymerase delta catalytic subunit isoform X2

    UniProtKB/TrEMBL
    A0A087WYJ2

  5. XM_017026882.3 → XP_016882371.1  DNA polymerase delta catalytic subunit isoform X2

    UniProtKB/TrEMBL
    A0A087WYJ2, A0A2R8Y705
    Related
    ENSP00000481858.2, ENST00000613923.6
    Conserved Domains (4) summary
    cd05777
    Location:304 → 533
    DNA_polB_delta_exo; DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase
    cd05533
    Location:579 → 950
    POLBc_delta; DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding ...
    PTZ00166
    Location:81 → 1076
    PTZ00166; DNA polymerase delta catalytic subunit; Provisional
    pfam14260
    Location:988 → 1058
    zf-C4pol; C4-type zinc-finger of DNA polymerase delta

  6. XM_005259008.5 → XP_005259065.1  DNA polymerase delta catalytic subunit isoform X2

    UniProtKB/TrEMBL
    A0A087WYJ2, A0A2R8Y705
    Conserved Domains (4) summary
    cd05777
    Location:304 → 533
    DNA_polB_delta_exo; DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase
    cd05533
    Location:579 → 950
    POLBc_delta; DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding ...
    PTZ00166
    Location:81 → 1076
    PTZ00166; DNA polymerase delta catalytic subunit; Provisional
    pfam14260
    Location:988 → 1058
    zf-C4pol; C4-type zinc-finger of DNA polymerase delta

  7. XM_011527038.2 → XP_011525340.1  DNA polymerase delta catalytic subunit isoform X1

    See identical proteins and their annotated locations for XP_011525340.1

    UniProtKB/Swiss-Prot
    P28340, Q8NER3, Q96H98
    UniProtKB/TrEMBL
    Q308M6
    Related
    ENSP00000472600.2, ENST00000601098.6
    Conserved Domains (1) summary
    PTZ00166
    Location:81 → 1100
    PTZ00166; DNA polymerase delta catalytic subunit; Provisional

  8. XM_047438950.1 → XP_047294906.1  DNA polymerase delta catalytic subunit isoform X2

    UniProtKB/TrEMBL
    A0A087WYJ2

RNA

  1. XR_935835.3 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060943.1 Alternate T2T-CHM13v2.0

    Range
    53471875..53505574
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054321233.1 → XP_054177208.1  DNA polymerase delta catalytic subunit isoform X1

    UniProtKB/Swiss-Prot
    P28340, Q8NER3, Q96H98

  2. XM_054321238.1 → XP_054177213.1  DNA polymerase delta catalytic subunit isoform X2

    UniProtKB/TrEMBL
    A0A087WYJ2

  3. XM_054321232.1 → XP_054177207.1  DNA polymerase delta catalytic subunit isoform X1

    UniProtKB/Swiss-Prot
    P28340, Q8NER3, Q96H98

  4. XM_054321236.1 → XP_054177211.1  DNA polymerase delta catalytic subunit isoform X2

    UniProtKB/TrEMBL
    A0A087WYJ2

  5. XM_054321237.1 → XP_054177212.1  DNA polymerase delta catalytic subunit isoform X2

    UniProtKB/TrEMBL
    A0A087WYJ2

  6. XM_054321235.1 → XP_054177210.1  DNA polymerase delta catalytic subunit isoform X2

    UniProtKB/TrEMBL
    A0A087WYJ2

  7. XM_054321234.1 → XP_054177209.1  DNA polymerase delta catalytic subunit isoform X1

    UniProtKB/Swiss-Prot
    P28340, Q8NER3, Q96H98

  8. XM_054321239.1 → XP_054177214.1  DNA polymerase delta catalytic subunit isoform X2

    UniProtKB/TrEMBL
    A0A087WYJ2

RNA

  1. XR_008485165.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
P28340.2 GenPept UniProtKB/Swiss-Prot:P28340

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