Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	5424
Gene name Gene Name - the full gene name approved by the HGNC.	DNA polymerase delta 1, catalytic subunit
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	POLD1
Synonyms (NCBI Gene) Gene synonyms aliases	CDC2, CRCS10, IMD120, MDPL, POLD
Chromosome Chromosome number	19
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	19q13.33
Summary Summary of gene provided in NCBI Entrez Gene.	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 ha

Show/Hide all(34)

SNP ID	Visualize variation	Clinical significance	Consequence
rs9282830	C>T	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, missense variant
rs41563714	C>G,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, non coding transcript variant, missense variant
rs45605236	C>T	Benign-likely-benign, likely-benign, conflicting-interpretations-of-pathogenicity, benign	Coding sequence variant, non coding transcript variant, synonymous variant
rs139949679	C>A,T	Likely-benign, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, synonymous variant, coding sequence variant
rs140160345	A>G	Likely-benign, conflicting-interpretations-of-pathogenicity	Intron variant
rs140216790	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity, benign-likely-benign	Non coding transcript variant, synonymous variant, coding sequence variant
rs140990974	C>T	Likely-benign, conflicting-interpretations-of-pathogenicity, benign-likely-benign	Missense variant, non coding transcript variant, coding sequence variant
rs144143245	G>C	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, non coding transcript variant, coding sequence variant
rs145473716	G>A	Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, genic downstream transcript variant, downstream transcript variant, non coding transcript variant, coding sequence variant
rs147911699	G>A,T	Uncertain-significance, likely-benign, conflicting-interpretations-of-pathogenicity	Missense variant, non coding transcript variant, coding sequence variant
rs149569984	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, non coding transcript variant, coding sequence variant
rs150010804	G>A,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Missense variant, non coding transcript variant, coding sequence variant
rs150066950	A>G,T	Likely-benign, conflicting-interpretations-of-pathogenicity, benign-likely-benign, benign	Missense variant, non coding transcript variant, coding sequence variant
rs199545019	G>A,C	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant, non coding transcript variant
rs199993010	T>C,G	Likely-benign, conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, coding sequence variant, non coding transcript variant
rs367680864	G>A	Conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, missense variant, coding sequence variant, non coding transcript variant
rs369332787	C>G,T	Likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, non coding transcript variant
rs369613619	G>A	Likely-benign, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, synonymous variant, coding sequence variant, non coding transcript variant
rs370478977	G>A,C,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Genic downstream transcript variant, downstream transcript variant, intron variant
rs375365167	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Intron variant
rs377690809	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, stop gained, non coding transcript variant
rs397514632	G>A	Pathogenic-likely-pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs398122386	CTC>-	Pathogenic	Inframe deletion, coding sequence variant, non coding transcript variant
rs587777627	T>C	Likely-pathogenic, pathogenic	Coding sequence variant, non coding transcript variant, missense variant
rs745850676	A>G	Conflicting-interpretations-of-pathogenicity, likely-benign	Synonymous variant, coding sequence variant, non coding transcript variant
rs753506843	G>A	Conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, intron variant
rs760140187	C>A,G,T	Likely-benign, conflicting-interpretations-of-pathogenicity	Intron variant, genic downstream transcript variant
rs760329559	CTC>-	Conflicting-interpretations-of-pathogenicity	Intron variant
rs761914051	C>A,G,T	Conflicting-interpretations-of-pathogenicity	Intron variant
rs762628311	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, intron variant, synonymous variant, genic downstream transcript variant
rs772468675	A>G,T	Benign-likely-benign, likely-benign, conflicting-interpretations-of-pathogenicity	Synonymous variant, coding sequence variant, intron variant, non coding transcript variant
rs775363857	G>A	Conflicting-interpretations-of-pathogenicity, likely-benign	Downstream transcript variant, intron variant, genic downstream transcript variant
rs1051057675	C>T	Conflicting-interpretations-of-pathogenicity, likely-benign	Coding sequence variant, genic downstream transcript variant, non coding transcript variant, synonymous variant
rs1555790184	T>C	Conflicting-interpretations-of-pathogenicity	Intron variant

Show/Hide all(18)

miRTarBase ID	miRNA	Experiments	Reference
MIRT004837	hsa-miR-24-3p	Luciferase reporter assay, Microarray, qRT-PCR, Western blot	19748357
MIRT004837	hsa-miR-24-3p	Luciferase reporter assay, Microarray, qRT-PCR, Western blot	19748357
MIRT016440	hsa-miR-193b-3p	Microarray	20304954
MIRT023874	hsa-miR-1-3p	Proteomics	18668040
MIRT025336	hsa-miR-34a-5p	Proteomics	21566225
MIRT025336	hsa-miR-34a-5p	Proteomics	21566225
MIRT051665	hsa-let-7e-5p	CLASH	23622248
MIRT043208	hsa-miR-324-5p	CLASH	23622248
MIRT2072888	hsa-miR-3189-5p	CLIP-seq
MIRT2072889	hsa-miR-4258	CLIP-seq
MIRT2072890	hsa-miR-4281	CLIP-seq
MIRT2072891	hsa-miR-4292	CLIP-seq
MIRT2072892	hsa-miR-4308	CLIP-seq
MIRT2072888	hsa-miR-3189-5p	CLIP-seq
MIRT2072889	hsa-miR-4258	CLIP-seq
MIRT2072890	hsa-miR-4281	CLIP-seq
MIRT2072891	hsa-miR-4292	CLIP-seq
MIRT2072892	hsa-miR-4308	CLIP-seq

Transcription factors

Show/Hide all(2)

Transcription factor	Regulation	Reference
SP1	Unknown	11375983
TP53	Unknown	11375983

Show/Hide all(64)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000109	Component	Nucleotide-excision repair complex	IDA	20713449
GO:0000166	Function	Nucleotide binding	IEA
GO:0000731	Process	DNA synthesis involved in DNA repair	IDA	3335506, 24191025
GO:0000731	Process	DNA synthesis involved in DNA repair	IEA
GO:0000731	Process	DNA synthesis involved in DNA repair	IMP	1730053
GO:0000781	Component	Chromosome, telomeric region	IDA	24270157
GO:0003676	Function	Nucleic acid binding	IEA
GO:0003677	Function	DNA binding	IDA	16762037
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	TAS	3146346
GO:0003682	Function	Chromatin binding	IDA	16762037, 24939902
GO:0003684	Function	Damaged DNA binding	IDA	24939902
GO:0003887	Function	DNA-directed DNA polymerase activity	IBA
GO:0003887	Function	DNA-directed DNA polymerase activity	IEA
GO:0003887	Function	DNA-directed DNA polymerase activity	IMP	16762037
GO:0003887	Function	DNA-directed DNA polymerase activity	TAS	9620226
GO:0004518	Function	Nuclease activity	IEA
GO:0004527	Function	Exonuclease activity	IEA
GO:0005515	Function	Protein binding	IPI	12403614, 15670210, 15805117, 16510448, 21044950, 23891004, 24191025, 24939902, 26496610, 28514442, 31449058, 32296183, 33961781, 35512704
GO:0005634	Component	Nucleus	IDA	16762037
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005829	Component	Cytosol	IDA
GO:0006260	Process	DNA replication	IEA
GO:0006260	Process	DNA replication	IMP	16762037
GO:0006260	Process	DNA replication	TAS	9620226
GO:0006261	Process	DNA-templated DNA replication	IBA
GO:0006261	Process	DNA-templated DNA replication	IDA	20334433
GO:0006261	Process	DNA-templated DNA replication	IEA
GO:0006281	Process	DNA repair	IEA
GO:0006281	Process	DNA repair	TAS	3146346
GO:0006287	Process	Base-excision repair, gap-filling	IBA
GO:0006287	Process	Base-excision repair, gap-filling	IDA	10559260, 10559261
GO:0006287	Process	Base-excision repair, gap-filling	IEA
GO:0006297	Process	Nucleotide-excision repair, DNA gap filling	IBA
GO:0006297	Process	Nucleotide-excision repair, DNA gap filling	IC	20713449
GO:0006297	Process	Nucleotide-excision repair, DNA gap filling	IMP	20227374
GO:0006974	Process	DNA damage response	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0008296	Function	3'-5'-DNA exonuclease activity	IBA
GO:0008408	Function	3'-5' exonuclease activity	IEA
GO:0009411	Process	Response to UV	TAS	3146346
GO:0016020	Component	Membrane	HDA	19946888
GO:0016235	Component	Aggresome	IDA
GO:0016740	Function	Transferase activity	IEA
GO:0016779	Function	Nucleotidyltransferase activity	IEA
GO:0016787	Function	Hydrolase activity	IEA
GO:0019899	Function	Enzyme binding	IEA
GO:0034061	Function	DNA polymerase activity	IEA
GO:0034644	Process	Cellular response to UV	IDA	24939902
GO:0043625	Component	Delta DNA polymerase complex	IBA
GO:0043625	Component	Delta DNA polymerase complex	IDA	11595739, 22465957
GO:0043625	Component	Delta DNA polymerase complex	IEA
GO:0043625	Component	Delta DNA polymerase complex	IPI	12403614
GO:0045004	Process	DNA replication proofreading	IBA
GO:0045004	Process	DNA replication proofreading	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0051536	Function	Iron-sulfur cluster binding	IEA
GO:0051539	Function	4 iron, 4 sulfur cluster binding	IEA
GO:0055089	Process	Fatty acid homeostasis	IMP	23770608
GO:0070987	Process	Error-free translesion synthesis	IDA	24191025
GO:0071897	Process	DNA biosynthetic process	IDA	11595739
GO:0071897	Process	DNA biosynthetic process	IEA

MIM	HGNC	e!Ensembl
174761	9175	ENSG00000062822

Protein

UniProt ID

P28340

Protein name

DNA polymerase delta catalytic subunit (EC 2.7.7.7) (3'-5' exodeoxyribonuclease) (EC 3.1.11.-) (DNA polymerase subunit delta p125)

Protein function

As the catalytic component of the trimeric (Pol-delta3 complex) and tetrameric DNA polymerase delta complexes (Pol-delta4 complex), plays a crucial role in high fidelity genome replication, including in lagging strand synthesis, and repair (PubM

PDB

6S1M , 6S1N , 6S1O , 6TNY , 6TNZ , 9EKB

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF03104	DNA_pol_B_exo1	130 → 477	DNA polymerase family B, exonuclease domain	Family
PF00136	DNA_pol_B	541 → 973	DNA polymerase family B	Family
PF14260	zf-C4pol	1012 → 1082	C4-type zinc-finger of DNA polymerase delta	Domain

Tissue specificity

TISSUE SPECIFICITY: Widely expressed, with high levels of expression in heart and lung. {ECO:0000269|PubMed:23770608}.

Sequence

MDGKRRPGPGPGVPPKRARGGLWDDDDAPRPSQFEEDLALMEEMEAEHRLQEQEEEELQS
VLEGVADGQVPPSAIDPRWLRPTPPALDPQTEPLIFQQLEIDHYVGPAQPVPGGPPPSRG
SVPVLRAFGVTDEGFSVCCHIHGFAPYFYTPAPPGFGPEHMGDLQRELNLAISRDSRGGR
ELTGPAVLAVELCSRESMFGYHGHGPSPFLRITVALPRLVAPARRLLEQGIRVAGLGTPS
FAPYEANVDFEIRFMVDTDIVGCNWLELPAGKYALRLKEKATQCQLEADVLWSDVVSHPP
EGPWQRIAPLRVLSFDIECAGRKGIFPEPERDPVIQICSLGLRWGEPEPFLRLALTLRPC
APILGAKVQSYEKEEDLLQAWSTFIRIMDPDVITGYNIQNFDLPYLISRAQTLKVQTFPF
LGRVAGLCSNIRDSSFQSKQTGRRDTKVVSMVGRVQMDMLQVLLREYKLRSYTLNAVSFH
FLGEQKEDVQHSIITDLQNGNDQTRRRLAVYCLKDAYLPLRLLERLMVLVNAVEMARVTG
VPLSYLLSRGQQVKVVSQLLRQAMHEGLLMPVVKSEGGEDYTGATVIEPLKGYYDVPIAT
LDFSSLYPSIMMAHNLCYTTLLRPGTAQKLGLTEDQFIRTPTGDEFVKTSVRKGLLPQIL
ENLLSARKRAKAELAKETDPLRRQVLDGRQLALKVSANSVYGFTGAQVGKLPCLEISQSV
TGFGRQMIEKTKQLVESKYTVENGYSTSAKVVYGDTDSVMCRFGVSSVAEAMALGREAAD
WVSGHFPSPIRLEFEKVYFPYLLISKKRYAGLLFSSRPDAHDRMDCKGLEAVRRDNCPLV
ANLVTASLRRLLIDRDPEGAVAHAQDVISDLLCNRIDISQLVITKELTRAASDYAGKQAH
VELAERMRKRDPGSAPSLGDRVPYVIISAAKGVAAYMKSEDPLFVLEHSLPIDTQYYLEQ
QLAKPLLRIFEPILGEGRAEAVLLRGDHTRCKTVLTGKVGGLLAFAKRRNCCIGCRTVLS
HQGAVCEFCQPRESELYQKEVSHLNALEERFSRLWTQCQRCQGSLHEDVICTSRDCPIFY
MRKKVRKDLEDQEQLLRRFGPPGPEAW

Sequence length

1107

Interactions

View interactions

	KEGG		Reactome
	DNA replication Base excision repair Nucleotide excision repair Mismatch repair Homologous recombination		Recognition of DNA damage by PCNA-containing replication complex Polymerase switching on the C-strand of the telomere Processive synthesis on the C-strand of the telomere Telomere C-strand (Lagging Strand) Synthesis Removal of the Flap Intermediate from the C-strand Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) PCNA-Dependent Long Patch Base Excision Repair Termination of translesion DNA synthesis HDR through Homologous Recombination (HRR) Gap-filling DNA repair synthesis and ligation in GG-NER Dual Incision in GG-NER Dual incision in TC-NER Gap-filling DNA repair synthesis and ligation in TC-NER Polymerase switching Removal of the Flap Intermediate Processive synthesis on the lagging strand

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
colorectal cancer	Colorectal cancer, susceptibility to, 10	rs397514632, rs398122386, rs587777627	N/A

Show/Hide Unknown Diseases (12)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Adenomatous Polyposis	polymerase proofreading-related adenomatous polyposis, Polymerase proofreading-related adenomatous polyposis	N/A	N/A	ClinVar, GenCC
Atrial Fibrillation	Atrial fibrillation	N/A	N/A	GWAS
Bile Duct Neoplasms	Bile duct cancer	N/A	N/A	ClinVar
Breast Cancer	Malignant tumor of breast	N/A	N/A	ClinVar
colon cancer	Colon cancer	N/A	N/A	ClinVar
Endometrial carcinoma	endometrial carcinoma	N/A	N/A	ClinVar
hereditary cancer	Hereditary cancer	N/A	N/A	ClinVar
Immunodeficiency	immunodeficiency 120	N/A	N/A	GenCC
Mandibular Hypoplasia, Deafness, Progeroid Features And Lipodystrophy Syndrome	mandibular hypoplasia-deafness-progeroid syndrome	N/A	N/A	GenCC
neoplasm	Neoplasm	N/A	N/A	ClinVar
Ovarian cancer	Familial ovarian cancer	N/A	N/A	ClinVar
Severe combined immunodeficiency disease	combined immunodeficiency, non-severe combined immunodeficiency due to polymerase delta deficiency	N/A	N/A	ClinVar, GenCC

Show/Hide Text Mining Associations (81)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Adenocarcinoma	Associate	32567205
Adenoma	Associate	25370038, 30827058
Adenomatous Polyposis Coli	Associate	28521875, 34140662, 35128723, 36291559, 37848928, 37990341
Adenomatous Polyps	Associate	32792570, 35620275
Allan Herndon Dudley syndrome	Associate	32567205
Alopecia	Associate	26172944
Aphasia Conduction	Associate	32792570
Attenuated familial adenomatous polyposis	Associate	31285513
Autoimmune Diseases	Associate	23245697
Brain Neoplasms	Associate	33948826, 35620275
Breast Neoplasms	Associate	17159154, 35351580, 35620275
Cafe au Lait Spots	Associate	27573199, 37990341
Carcinoma Non Small Cell Lung	Associate	32342665, 37345618
Carcinoma Renal Cell	Associate	35478106, 37095444
Central Nervous System Neoplasms	Associate	28976792
Colonic Neoplasms	Associate	36703617
Colonic Polyps	Associate	30827058
Colorectal Neoplasms	Associate	23528559, 25241845, 25370038, 25827231, 28368425, 28423643, 28521875, 29120461, 30683709, 30827058, 31857678, 32567205, 32792570, 33948826, 34250404 View all (6 more)
Colorectal Neoplasms Hereditary Nonpolyposis	Associate	26648449, 31297992, 31857678, 36291559, 38191122
Contracture	Associate	26172944
Cutis Laxa Autosomal Recessive Type IIB	Associate	26172944, 28521875, 31750734, 35196257, 35590056, 35620275, 36280868
Deafness	Associate	26172944, 28521875, 31944473, 35196257, 35590056, 35620275, 36280868
Drug Hypersensitivity	Associate	31750734
Dyslexia	Associate	33948826
Endometrial Neoplasms	Associate	23447401, 23528559, 25827231, 26755646, 28368425, 32792570, 33948826, 35620275, 38191122, 38231514
Fetal Alcohol Spectrum Disorders	Associate	31449058
Gallbladder Neoplasms	Associate	33328484
Genetic Diseases Inborn	Associate	31449058
Glioblastoma	Associate	28912153, 37990341
Glioma	Associate	37990341
Growth Disorders	Associate	26172944
Hearing Loss	Associate	31944473
Hearing Loss Sensorineural	Associate	36280868
Hepatolenticular Degeneration	Associate	39809184
Immunologic Deficiency Syndromes	Associate	31449058
Intestinal Polyposis	Associate	27573199, 29367705, 32792570, 36856825
Kidney Neoplasms	Associate	37095444
Leukemia Myeloid Acute	Associate	39768855
Lipodystrophy	Associate	28521875, 33618333, 35590056, 35620275, 36280868
Lipodystrophy Familial Partial	Associate	28199729
Liposarcoma	Associate	35002543
Lung Neoplasms	Associate	31673068
Lymphopenia	Associate	31629014
Male Infertility with Large Headed Multiflagellar Polyploid Spermatozoa	Associate	24803180
Mandibular Diseases	Associate	26172944, 28521875, 31750734, 33618333, 35196257, 35590056, 35620275, 36280868
Mesothelioma	Associate	22905093
Metabolic Diseases	Associate	26172944, 31944473
Microsatellite Instability	Associate	31769227, 34250404
Mood Disorders	Associate	28199729
Multiple Myeloma	Associate	36861411
Neoplasm Metastasis	Associate	37105989
Neoplasms	Associate	11375983, 11891323, 19966286, 23447401, 25194673, 25827231, 26648449, 26755646, 27573199, 28368425, 28423643, 28512192, 28976792, 29763623, 30257222 View all (23 more)
Neoplasms Squamous Cell	Associate	24114512
Neoplastic Syndromes Hereditary	Associate	32792570, 34285382, 37848928
Nervous System Diseases	Associate	33618333
Neuroblastoma	Associate	9348340
Nonsyndromic sensorineural hearing loss	Associate	31944473
Oligodendroglioma	Associate	37990341
Ovarian Neoplasms	Associate	32762026, 33948826
Pancreatic Cyst	Associate	31576098
Pilomatrixoma	Associate	27573199
Polyposis Syndrome Hereditary Mixed 1	Associate	23447401, 30827058, 34285382
Precancerous Conditions	Associate	37105989
Precursor Cell Lymphoblastic Leukemia Lymphoma	Associate	29768346
Proctocolitis	Associate	27573199
Prodromal Symptoms	Associate	37345618
Progeroid syndrome neonatal	Associate	26172944, 31750734
Prostatic Neoplasms	Associate	37950047
Prostatic Neoplasms Castration Resistant	Associate	37950047
Sarcoma Endometrial Stromal	Associate	32792570
Strabismus	Associate	35196257
T cell immunodeficiency primary	Associate	31629014
Triple Negative Breast Neoplasms	Associate	36001024
Turcot syndrome	Associate	27573199, 28368425, 35002543, 36291559
Urinary Bladder Neoplasms	Associate	37105989
Uterine Cervical Neoplasms	Associate	19389243
Uterine Diseases	Associate	33948826
Werner Syndrome	Associate	10781066, 22351772, 26172944
Werner Syndrome	Stimulate	22787159
X Linked Combined Immunodeficiency Diseases	Associate	31629014
Zinc Deficiency Neonatal due to Low Breast Milk Zinc	Inhibit	30427259

POLD1 (DNA polymerase delta 1, catalytic subunit)