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

Gene ID: 5424, updated on 26-Jul-2021

Summary

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
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
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Genomic context

See POLD1 in Genome Data Viewer
Location:
19q13.33
Exon count:
30
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (50384291..50418018)
105.20201022 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 napsin A aspartic peptidase Neighboring gene nuclear receptor subfamily 1 group H member 2 Neighboring gene Spi-B transcription factor Neighboring gene myosin binding protein C2

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

Associated conditions

Description Tests
Colorectal cancer 10
MedGen: C2675481 OMIM: 612591 GeneReviews: Not available
Compare labs
Mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome
MedGen: C3715192 OMIM: 615381 GeneReviews: Not available
Compare labs
Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
GeneReviews: Not available

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 3'-5'-exodeoxyribonuclease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
PubMed 
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-dependent DNA replication IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
involved_in base-excision repair, gap-filling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 nucleic acid phosphodiester bond hydrolysis IEA
Inferred from Electronic Annotation
more info
 
involved_in nucleotide-excision repair, DNA gap filling IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
part_of delta DNA polymerase complex IDA
Inferred from Direct Assay
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

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_016882370.1
XP_016882371.1

NCBI Reference Sequences (RefSeq)

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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_001256849.1NP_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
    UniProtKB/TrEMBL
    A0A024R4F4
    Related
    ENSP00000473052.1, ENST00000599857.7
    Conserved Domains (1) summary
    PTZ00166
    Location:811100
    PTZ00166; DNA polymerase delta catalytic subunit; Provisional
  2. NM_001308632.1NP_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:304533
    DNA_polB_delta_exo; DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase
    cd05533
    Location:5791000
    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:811126
    PTZ00166; DNA polymerase delta catalytic subunit; Provisional
    pfam14260
    Location:10381108
    zf-C4pol; C4-type zinc-finger of DNA polymerase delta
  3. NM_002691.4NP_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
    UniProtKB/TrEMBL
    A0A024R4F4, Q59FA0
    Related
    ENSP00000406046.1, ENST00000440232.7
    Conserved Domains (1) summary
    PTZ00166
    Location:811100
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

    Range
    50384291..50418018
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005259008.4XP_005259065.1  DNA polymerase delta catalytic subunit isoform X2

    Conserved Domains (4) summary
    cd05777
    Location:304533
    DNA_polB_delta_exo; DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase
    cd05533
    Location:579950
    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:811076
    PTZ00166; DNA polymerase delta catalytic subunit; Provisional
    pfam14260
    Location:9881058
    zf-C4pol; C4-type zinc-finger of DNA polymerase delta
  2. XM_017026882.2XP_016882371.1  DNA polymerase delta catalytic subunit isoform X2

    Related
    ENSP00000481858.2, ENST00000613923.6
    Conserved Domains (4) summary
    cd05777
    Location:304533
    DNA_polB_delta_exo; DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase
    cd05533
    Location:579950
    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:811076
    PTZ00166; DNA polymerase delta catalytic subunit; Provisional
    pfam14260
    Location:9881058
    zf-C4pol; C4-type zinc-finger of DNA polymerase delta
  3. XM_017026881.1XP_016882370.1  DNA polymerase delta catalytic subunit isoform X1

    UniProtKB/Swiss-Prot
    P28340
    UniProtKB/TrEMBL
    A0A024R4F4
    Conserved Domains (1) summary
    PTZ00166
    Location:811100
    PTZ00166; DNA polymerase delta catalytic subunit; Provisional
  4. XM_011527038.1XP_011525340.1  DNA polymerase delta catalytic subunit isoform X1

    See identical proteins and their annotated locations for XP_011525340.1

    UniProtKB/Swiss-Prot
    P28340
    UniProtKB/TrEMBL
    A0A024R4F4
    Related
    ENSP00000472600.2, ENST00000601098.6
    Conserved Domains (1) summary
    PTZ00166
    Location:811100
    PTZ00166; DNA polymerase delta catalytic subunit; Provisional

RNA

  1. XR_935835.2 RNA Sequence

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