POLK

gene
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Also known as POLQDINP

Summary

POLK (DNA polymerase kappa, HGNC:9183) is a protein-coding gene on chromosome 5q13.3, encoding DNA polymerase kappa (Q9UBT6). DNA polymerase specifically involved in DNA repair.

This gene encodes a member of the DNA polymerase type-Y family of proteins. The encoded protein is a specialized DNA polymerase that catalyzes translesion DNA synthesis, which allows DNA replication in the presence of DNA lesions. Human cell lines lacking a functional copy of this gene exhibit impaired genome integrity and enhanced susceptibility to oxidative damage. Mutations in this gene that impair enzyme activity may be associated with prostate cancer in human patients.

Source: NCBI Gene 51426 — RefSeq curated summary.

At a glance

  • GWAS associations: 4
  • Clinical variants (ClinVar): 138 total — 19 pathogenic
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • Cancer driver (intOGen): loss-of-function (tumor-suppressor-like) across 3 cancer types
  • MANE Select transcript: NM_016218

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9183
Approved symbolPOLK
NameDNA polymerase kappa
Location5q13.3
Locus typegene with protein product
StatusApproved
AliasesPOLQ, DINP
Ensembl geneENSG00000122008
Ensembl biotypeprotein_coding
OMIM605650
Entrez51426

Gene structure

Transcript identifiers

Ensembl transcripts: 24 — 12 protein_coding, 7 nonsense_mediated_decay, 3 retained_intron, 2 protein_coding_CDS_not_defined

ENST00000241436, ENST00000502567, ENST00000503479, ENST00000504026, ENST00000505069, ENST00000505774, ENST00000505975, ENST00000506928, ENST00000507073, ENST00000508526, ENST00000508867, ENST00000509126, ENST00000510815, ENST00000511527, ENST00000514141, ENST00000514296, ENST00000515295, ENST00000863893, ENST00000863894, ENST00000863895, ENST00000863896, ENST00000935335, ENST00000965054, ENST00000965055

RefSeq mRNA: 13 — MANE Select: NM_016218 NM_001345921, NM_001345922, NM_001387110, NM_001387111, NM_001387113, NM_001395893, NM_001395894, NM_001395897, NM_001395899, NM_001395900, NM_001395901, NM_001395902, NM_016218

CCDS: CCDS4030

Canonical transcript exons

ENST00000241436 — 15 exons

ExonStartEnd
ENSE000019058137559793475609991
ENSE000020428887551189175511914
ENSE000034690087556934075569492
ENSE000035089057557678075576933
ENSE000035140527559774775597789
ENSE000035382937558476075584926
ENSE000035462327558329375583417
ENSE000035510807559622275597178
ENSE000035569007558702675587058
ENSE000036052737558120975581448
ENSE000036099567554701075547157
ENSE000036157617557373875573869
ENSE000036219797555247275552591
ENSE000036330497559387875594049
ENSE000036551867559034475590440

Expression profiles

Bgee: expression breadth ubiquitous, 255 present calls, max score 95.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 14.2360 / max 814.1123, expressed in 1732 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
5708613.34741720
570870.7997405
570880.089036

Top tissues by expression

259 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
calcaneal tendonUBERON:000370195.55gold quality
adrenal tissueUBERON:001830392.41gold quality
corpus callosumUBERON:000233691.26gold quality
superficial temporal arteryUBERON:000161490.93gold quality
colonic epitheliumUBERON:000039790.86gold quality
mucosa of paranasal sinusUBERON:000503090.40gold quality
oviduct epitheliumUBERON:000480489.91gold quality
skin of hipUBERON:000155489.71gold quality
trabecular bone tissueUBERON:000248389.06gold quality
monocyteCL:000057688.43gold quality
islet of LangerhansUBERON:000000688.28gold quality
layer of synovial tissueUBERON:000761687.95gold quality
leukocyteCL:000073887.87gold quality
bone marrow cellCL:000209287.83gold quality
lower lobe of lungUBERON:000894987.62gold quality
jejunal mucosaUBERON:000039987.60gold quality
smooth muscle tissueUBERON:000113587.24gold quality
jejunumUBERON:000211586.91gold quality
pigmented layer of retinaUBERON:000178286.55gold quality
retinaUBERON:000096686.53gold quality
Brodmann (1909) area 46UBERON:000648386.30gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047385.62gold quality
subcutaneous adipose tissueUBERON:000219085.51gold quality
adipose tissueUBERON:000101385.49gold quality
popliteal arteryUBERON:000225085.45gold quality
tibial arteryUBERON:000761085.45gold quality
spermCL:000001985.31gold quality
urinary bladderUBERON:000125585.09gold quality
myocardiumUBERON:000234984.99silver quality
synovial jointUBERON:000221784.96gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes7.65
E-GEOD-36552no67.79

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): AHR, ELF4, HSF1, TP53

miRNA regulators (miRDB)

121 targeting POLK, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-3163100.0077.238605
HSA-MIR-429100.0073.442698
HSA-MIR-200B-3P100.0073.312693
HSA-MIR-200C-3P100.0073.352685
HSA-MIR-5692A100.0074.406850
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-3646100.0073.565283
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-340-5P100.0072.504437
HSA-MIR-126-5P100.0072.713180
HSA-MIR-656-3P100.0072.152788
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-4795-3P100.0074.624024
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-548N99.9871.944170
HSA-MIR-512-3P99.9767.351049
HSA-MIR-9-3P99.9670.882068
HSA-MIR-493-5P99.9672.472382
HSA-MIR-302E99.9670.742669
HSA-MIR-590-3P99.9674.346478
HSA-MIR-570-3P99.9672.414910
HSA-MIR-365899.9673.874379

Literature-anchored findings (GeneRIF, showing 40)

  • a role of Pol(kappa) in the extension of mismatched base pairs during normal DNA replication, and in addition, they implicate Pol(kappa) in the mutagenic bypass of T-T dimers (PMID:11842189)
  • Translesion synthesis by human DNA polymerase kappa on a DNA template containing a single stereoisomer of dG-(+)- or dG-(-)-anti-N(2)-BPDE. (PMID:11994005)
  • In DNA damage, this protein bypasses and extends beyond thymine glycols during DNA synthesis in vitro, preferentially incorporating correct nucleotides (PMID:12145297)
  • Polkappa may function as part of the replication machinery itself and could be recruited when replicative complexes are stalled; may affect the accuracy of DNA replication (PMID:12414988)
  • Opposite an 8-oxoguanine (8-oxoG) lesion, Polkappa efficiently inserts an A & then proficiently extends from it. Also, Polkappa can perform the extension step after the incorporation of nucleotides opposite these lesion sites by Poldelta. (PMID:12444249)
  • Data suggest that the properties of DNA polymerases eta and kappa are consistent with the mutagenic events attributed to estrogen-derived DNA adducts. (PMID:15147214)
  • POLK interacts with a C-terminal region of REV1. (PMID:15189446)
  • Poliota incorporates a C opposite the gamma-HOPdG adduct with nearly the same efficiency as opposite a nonadducted G residue. The subsequent extension step is performed by Polkappa, which efficiently extends from the C incorporated opposite the adduct. (PMID:15199127)
  • POLK does not colocalize in replication foci with PCNA. (PMID:15601657)
  • the trans-lesion synthesis enzyme polkappa is specifically required for normal recovery from the BPDE-induced S-phase checkpoint (PMID:15817457)
  • POLK causes error-prone and inefficient replication across 8-oxoguanine in ras genes. (PMID:15938713)
  • DNA polymerase kappa (Pol kappa) is a specialised low-fidelity DNA polymerase. It is able to perform DNA synthesis across several damaged bases. But when it is misregulated, it will increase genetic instability. (PMID:15989980)
  • both Poleta and Polkappa rely on W-C hydrogen bonding for localizing the nascent base pair in the active site for the polymerization reaction to occur (PMID:16055723)
  • The sequential action of Poliota and Polkappa promotes efficient and error-free synthesis through the HNE-dG adducts. (PMID:16354708)
  • Association of Polkappa with PCNA is regulated by Rad18-mediated PCNA ubiquitination. (PMID:16611994)
  • pol kappa is resistant to N(2)-bulk and quantitatively efficient in catalyzing dCTP incorporation opposite bulky guanine N(2)-adducts, particularly the largest (N(2)-BPG) (PMID:16751196)
  • promoter of POLK is cis-controlled (PMID:17099721)
  • DNA encirclement and other structural features help explain Pol kappa’s ability to extend mismatches and to promote replication through various minor groove DNA lesions. (PMID:17317631)
  • Human DNA polymerase kappa inserts dGMP and dCMP within the T mononucleotide repeat, producing an interrupted 12-bp allele. (PMID:18079151)
  • Data show that showed that pol kappaDeltaC was more efficient than pol eta by incorporating dCMP opposite both 6alpha- and 6beta-isomeric dG-N(2)-6-E(2) adducts. (PMID:18512958)
  • Results show that the DNA polymerase kappa N-clasp is a key structural feature that accounts for the dA adduct blockage and the near-error-free bypass of the dG lesion. (PMID:18931375)
  • Downregulation of DNA polymerases kappa is associated with colorectal-adenocarcinomas. (PMID:19117014)
  • Y-Family DNA polymerases may use two different dNTP shapes for insertion: a hypothesis and its implications. (PMID:19188081)
  • steric gate amino acid tyrosine 112 is required for efficient mismatched-primer extension by human DNA polymerase kappa (PMID:19341290)
  • structure of human DNA polymerase kappa with dATP opposite the 8-OxoG DNA lesion (PMID:19492058)
  • analysis of the mechanism promoting error-prone synthesis by human DNA polymerase kappa opposite the 7,8-dihydro-8-oxo-2’-deoxyguanosine a (PMID:19542228)
  • Translesional DNA synthesis through a C8-guanyl adduct of 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP) in Vitro: REV1 inserts dC opposite the lesion, and DNA polymerase kappa potentially catalyzes extension reaction from the 3’-dC terminus. (PMID:19628463)
  • results suggested that amino acids at distinct positions in the active sites of Poleta and Polkappa might enhance 8-oxo-dGTP to favor the syn conformation, and thus direct its misincorporation into DNA. (PMID:19939936)
  • The expression of Pol kappa (and Pol iota) is deregulated in gliomas, and upregulation of Pol kappa is associated with poorer prognosis in glioma patients. (PMID:20164241)
  • the substitution of alanine for phenylalanine 171 (F171), an amino acid conserved between Pol kappa and its bacterial counterpart Escherichia coli DinB, enhanced the efficiencies of dCMP incorporation opposite (-)- and (+)-trans-anti-BPDE-N(2)-dG 18-fold (PMID:21078407)
  • in mammalian cells, both polymerases kappa and iota are necessary for the error-free bypass of N(2)-CEdG and N(2)-CMdG. (PMID:21454642)
  • show that the loss of USP1 leads to a dramatic reduction of replication fork speed in a Polkappa-dependent manner (PMID:22157819)
  • transcriptional activities of the POLK promoter regions -336/+437 and +20/+437 were significantly reduced by BPDE treatment, indicating that transcription factors in these regions may regulate the transcription of human POLK gene in response to BPDE. (PMID:22227292)
  • Data suggest that DNA polymerase kappa (pol kappa) partially protects cells from the mismatch repair (MMR)-dependent cytotoxicity. (PMID:22487424)
  • Molecular dynamics simulations show that the near error-free incorporation of dCTP opposite the major benzo[a]pyrene-derived dG lesion is compatible with the Water Mediated and Substrate Assisted (WMSA) mechanism, allowing for an essentially undisturbed pentacovalent phosphorane transition state, and explaining the bypass of this lesion with little mutation by Pol kappa. (PMID:22772988)
  • Data indicate that small molecule library screens targeting DNA polymerase kappa would initiate the development of new adjunct cancer therapeutics. (PMID:23056190)
  • The results show that hPolkappa uses a classical Streisinger template-slippage mechanism to generate -1 deletions in repetitive sequences. (PMID:23558743)
  • Pol eta and Pol kappa are involved in redundant pathways for homologous recombination. (PMID:23731732)
  • DNA polymerase kappa-dependent DNA synthesis at stalled replication forks is important for CHK1 activation. (PMID:23799366)
  • DNA polymerase kappa rs5744724 polymorphism is associated with lung cancer. (PMID:24012694)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriopolkENSDARG00000059963
mus_musculusPolkENSMUSG00000021668
rattus_norvegicusPolkENSRNOG00000060626
drosophila_melanogasterecoFBGN0035766
caenorhabditis_elegansWBGENE00017696

Paralogs (5): POLI (ENSG00000101751), REV1 (ENSG00000135945), ESCO1 (ENSG00000141446), POLH (ENSG00000170734), ESCO2 (ENSG00000171320)

Protein

Protein identifiers

DNA polymerase kappaQ9UBT6 (reviewed: Q9UBT6)

Alternative names: DINB protein

All UniProt accessions (5): D6R9M8, D6RAE5, D6RAI7, D6RDX9, Q9UBT6

UniProt curated annotations — full annotation on UniProt →

Function. DNA polymerase specifically involved in DNA repair. Plays an important role in translesion synthesis, where the normal high-fidelity DNA polymerases cannot proceed and DNA synthesis stalls. Depending on the context, it inserts the correct base, but causes frequent base transitions, transversions and frameshifts. Lacks 3’-5’ proofreading exonuclease activity. Forms a Schiff base with 5’-deoxyribose phosphate at abasic sites, but does not have lyase activity.

Subunit / interactions. Interacts with REV1. Forms a quaternary complex with REV1, MAD2L2 and REV3L, where REV3L-bound MAD2L2 and POLK are able to bind simultaneously to REV1 forming the stable translesion synthesis (TLS) machinery therefore bridging the inserter and extender polymerases. Interacts with PCNA.

Subcellular location. Nucleus.

Tissue specificity. Detected at low levels in testis, spleen, prostate and ovary. Detected at very low levels in kidney, colon, brain, heart, liver, lung, placenta, pancreas and peripheral blood leukocytes.

Cofactor. Divalent metal cations. Prefers Mg(2+), but can also use Mn(2+).

Domain organisation. The catalytic core consists of fingers, palm and thumb subdomains, but the fingers and thumb subdomains are much smaller than in high-fidelity polymerases; residues from five sequence motifs of the Y-family cluster around an active site cleft that can accommodate DNA and nucleotide substrates with relaxed geometric constraints, with consequently higher rates of misincorporation and low processivity.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the DNA polymerase type-Y family.

Isoforms (8)

UniProt IDNamesCanonical?
Q9UBT6-11yes
Q9UBT6-22
Q9UBT6-33
Q9UBT6-44
Q9UBT6-55
Q9UBT6-66
Q9UBT6-77
Q9UBT6-88

RefSeq proteins (13): NP_001332850, NP_001332851, NP_001374039, NP_001374040, NP_001374042, NP_001382822, NP_001382823, NP_001382826, NP_001382828, NP_001382829, NP_001382830, NP_001382831, NP_057302* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001126UmuCDomain
IPR006642Rad18_UBZ4Domain
IPR017961DNA_pol_Y-fam_little_fingerDomain
IPR022880DNApol_IVFamily
IPR024728PolY_HhH_motifConserved_site
IPR036775DNA_pol_Y-fam_lit_finger_sfHomologous_superfamily
IPR043128Rev_trsase/Diguanyl_cyclaseHomologous_superfamily
IPR043502DNA/RNA_pol_sfHomologous_superfamily
IPR050116DNA_polymerase-YFamily

Pfam: PF00817, PF11798, PF11799

Enzyme classification (BRENDA):

  • EC 2.7.7.7 — DNA-directed DNA polymerase (BRENDA: 139 organisms, 372 substrates, 325 inhibitors, 281 Km, 239 kcat entries)

Substrate kinetics (BRENDA)

52 substrates with measured Km, best-characterized 15. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
DATP0.0003–3.252
DCTP0.0001–2.546
DTTP0.0003–47.446
DGTP0.0002–2.529
DEOXYNUCLEOSIDE TRIPHOSPHATE0.0012–0.6412
DNAN7
7-DEAZA-2’-DEOXYADENOSINE 5’-TRIPHOSPHATE0.0011–0.3445
N1-METHYL-2’-DEOXYADENOSINE 5’-TRIPHOSPHATE0.223–0.4035
2-AMINOPURINE-2’-DEOXY-D-RIBOSE 5’-TRIPHOSPHATE0.006–0.01442
2-THIO-DCTP0.067–0.982
5-METHYL-DCTP0.013–1.222
DAMP:DG1.153–1.422
DCMP:DG2
DGMP:DG0.263–0.35112
DTMP:DG1.26–1.432

Catalyzed reactions (Rhea), 1 shown:

  • DNA(n) + a 2’-deoxyribonucleoside 5’-triphosphate = DNA(n+1) + diphosphate (RHEA:22508)

UniProt features (82 total): helix 23, strand 15, binding site 11, splice variant 10, sequence conflict 6, sequence variant 5, turn 5, zinc finger region 2, mutagenesis site 2, chain 1, domain 1, region of interest 1

Structure

Experimental structures (PDB)

19 structures.

PDBMethodResolution (Å)
6CSTX-RAY DIFFRACTION2
1T94X-RAY DIFFRACTION2.4
5W2CX-RAY DIFFRACTION2.5
4U6PX-RAY DIFFRACTION2.59
4BA9X-RAY DIFFRACTION2.73
4U7CX-RAY DIFFRACTION2.8
6BRXX-RAY DIFFRACTION2.8
5W2AX-RAY DIFFRACTION2.9
5T14X-RAY DIFFRACTION3
2OH2X-RAY DIFFRACTION3.05
6BS1X-RAY DIFFRACTION3.15
2W7OX-RAY DIFFRACTION3.16
3IN5X-RAY DIFFRACTION3.2
4GK5X-RAY DIFFRACTION3.21
3PZPX-RAY DIFFRACTION3.34
7NV0ELECTRON MICROSCOPY3.4
2W7PX-RAY DIFFRACTION3.71
7NV1ELECTRON MICROSCOPY6.4
2LSISOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9UBT6-F170.620.49

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (11): 642; 646; 779; 782; 797; 801; 107; 198; 199; 624; 627

Mutagenesis-validated functional residues (2):

PositionPhenotype
198loss of dna polymerase activity; when associated with a-199.
199loss of dna polymerase activity; when associated with d-198.

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

IDPathway
R-HSA-5655862Translesion synthesis by POLK
R-HSA-5656169Termination of translesion DNA synthesis
R-HSA-5685942HDR through Homologous Recombination (HRR)
R-HSA-5696397Gap-filling DNA repair synthesis and ligation in GG-NER
R-HSA-5696400Dual Incision in GG-NER
R-HSA-6782135Dual incision in TC-NER
R-HSA-6782210Gap-filling DNA repair synthesis and ligation in TC-NER

MSigDB gene sets: 394 (showing top): GOBP_DNA_TEMPLATED_DNA_REPLICATION_MAINTENANCE_OF_FIDELITY, GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR, GOBP_RNA_TEMPLATED_DNA_BIOSYNTHETIC_PROCESS, RNGTGGGC_UNKNOWN, RRAGTTGT_UNKNOWN, GOBP_REGULATION_OF_DNA_RECOMBINATION, KANG_DOXORUBICIN_RESISTANCE_UP, GOBP_CELLULAR_RESPONSE_TO_UV, TGCACTT_MIR519C_MIR519B_MIR519A, GOBP_CELLULAR_RESPONSE_TO_LIGHT_STIMULUS, GOBP_NEGATIVE_REGULATION_OF_DNA_REPAIR, GOBP_NEGATIVE_REGULATION_OF_DNA_RECOMBINATION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GEORGES_CELL_CYCLE_MIR192_TARGETS, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP

GO Biological Process (8): DNA replication (GO:0006260), DNA repair (GO:0006281), nucleotide-excision repair, DNA gap filling (GO:0006297), DNA damage response (GO:0006974), translesion synthesis (GO:0019985), cellular response to UV (GO:0034644), error-prone translesion synthesis (GO:0042276), DNA biosynthetic process (GO:0071897)

GO Molecular Function (8): damaged DNA binding (GO:0003684), DNA-directed DNA polymerase activity (GO:0003887), zinc ion binding (GO:0008270), DNA binding (GO:0003677), transferase activity (GO:0016740), nucleotidyltransferase activity (GO:0016779), DNA polymerase activity (GO:0034061), metal ion binding (GO:0046872)

GO Cellular Component (4): nucleus (GO:0005634), nucleoplasm (GO:0005654), nuclear body (GO:0016604), site of DNA damage (GO:0090734)

Reactome top-level categories

Rollup of top-4 pathways:

CategoryPathways
Translesion synthesis by Y family DNA polymerases bypasses lesions on DNA template2
Global Genome Nucleotide Excision Repair (GG-NER)2
Transcription-Coupled Nucleotide Excision Repair (TC-NER)2
HDR through Homologous Recombination (HRR) or Single Strand Annealing (SSA)1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
DNA metabolic process4
DNA biosynthetic process2
cellular anatomical structure2
DNA damage response1
nucleotide-excision repair1
cellular response to stress1
DNA damage tolerance1
DNA synthesis involved in DNA replication1
response to UV1
cellular response to light stimulus1
translesion synthesis1
nucleic acid biosynthetic process1
DNA binding1
DNA polymerase activity1
transition metal ion binding1
nucleic acid binding1
catalytic activity1
transferase activity, transferring phosphorus-containing groups1
nucleotidyltransferase activity1
catalytic activity, acting on DNA1
cation binding1
intracellular membrane-bounded organelle1
nuclear lumen1
nucleoplasm1
intracellular membraneless organelle1
chromosome1

Protein interactions and networks

STRING

1302 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
POLKPOLLQ9UGP5754
POLKREV3LO60673717
POLKPOLMQ9NP87644
POLKRAD51Q06609605
POLKPOLQO75417586
POLKPOLHQ9Y253577
POLKPOLNQ7Z5Q5559
POLKPOLD2P49005555
POLKMAD2L2Q9UI95514
POLKREV1Q9UBZ9463
POLKRAD18Q9NS91446
POLKPOLD1P28340433
POLKPOLIQ9UNA4420
POLKCLPBQ9H078408
POLKUNGP13051399

IntAct

22 interactions, top by confidence:

ABTypeScore
PARVGLIMS1psi-mi:“MI:0914”(association)0.640
SPARTITCHpsi-mi:“MI:0914”(association)0.640
KCTD17CBX4psi-mi:“MI:0914”(association)0.530
POLKHSP90B1psi-mi:“MI:0915”(physical association)0.400
POLKHSPA5psi-mi:“MI:0915”(physical association)0.400
POLKLMNApsi-mi:“MI:0915”(physical association)0.400
POLKH3-4psi-mi:“MI:0915”(physical association)0.400
DTD1POLKpsi-mi:“MI:0915”(physical association)0.400
KCTD2POLKpsi-mi:“MI:0915”(physical association)0.400
RhoaCLK2psi-mi:“MI:0914”(association)0.350
Kctd5psi-mi:“MI:0914”(association)0.350
POLKTIA1psi-mi:“MI:0914”(association)0.350
KCTD17CBX4psi-mi:“MI:0914”(association)0.350
RBM39RPS3Apsi-mi:“MI:0914”(association)0.350
KCTD17PXDNLpsi-mi:“MI:0914”(association)0.350
SLC1A3DDX11L8psi-mi:“MI:0914”(association)0.350
POLKpsi-mi:“MI:0915”(physical association)0.000

BioGRID (549): POLK (Affinity Capture-MS), POLK (Affinity Capture-MS), H3F3A (Affinity Capture-MS), RAD51 (Affinity Capture-MS), RBM4 (Affinity Capture-MS), STAT6 (Affinity Capture-MS), TIA1 (Affinity Capture-MS), UBE2V2 (Affinity Capture-MS), PIAS1 (Affinity Capture-MS), NOLC1 (Affinity Capture-MS), SRA1 (Affinity Capture-MS), CD2BP2 (Affinity Capture-MS), APOL2 (Affinity Capture-MS), RPAP1 (Affinity Capture-MS), KCTD5 (Affinity Capture-MS)

ESM2 similar proteins: A0A1P8ASY1, A3EWL3, A4PBL4, B9EUM5, B9FL70, B9G8P1, F4HZF0, F4I9Q5, F4IL57, F4J2M6, F4JAA5, L0N7N1, O09053, O70445, O81635, O93530, P35251, P39875, P45951, Q0IMS9, Q0PCS3, Q10MN5, Q14191, Q3YK19, Q5SXJ3, Q6JDV7, Q6P158, Q7X7H4, Q7Y1C4, Q7Y1C5, Q803U7, Q8L7Y8, Q8L840, Q8W1Y3, Q941I6, Q99728, Q9C6G0, Q9FT70, Q9FT72, Q9I920

Diamond homologs: A0AK80, A0KHD5, A0KTR5, A0Q6K9, A1A7U2, A1KUQ3, A1U339, A1WY69, A2RNH9, A3N148, A4TPK8, A4W6W8, A5FSS1, A5IH02, A6W1V6, A7FLI9, A7MEN4, A7NC07, A7ZHZ2, A7ZWJ6, A8AKQ2, A8FYV3, A9MNS1, A9MY13, B0BPX9, B0TZS5, B1AJ79, B1J100, B1KD33, B1YK83, B2FLR2, B2SH34, B2U3S3, B4SIF5, B8DBV7, B8F542, B8FBE8, C1KWR9, O74944, P34409

SIGNOR signaling

0 interactions.

Disease & clinical

Cancer significance

From intOGen — cancer-driver classification: loss-of-function (tumor-suppressor-like) across 3 cancer types — LUSC, MEL, UCEC.

Clinical variants and AI predictions

ClinVar

138 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic19
Likely pathogenic0
Uncertain significance93
Likely benign8
Benign1

Top pathogenic / likely-pathogenic (19)

Variant IDHGVSClassification
190430NM_016218.6(POLK):c.*66T>CPathogenic
218216NM_016218.6(POLK):c.1256A>G (p.Glu419Gly)Pathogenic
218217NM_016218.6(POLK):c.1284G>A (p.Ala428=)Pathogenic
218218NM_016218.6(POLK):c.1324C>T (p.Leu442Phe)Pathogenic
218219NM_016218.6(POLK):c.1289A>G (p.Glu430Gly)Pathogenic
218220NM_016218.6(POLK):c.1341G>A (p.Gln447=)Pathogenic
218221NM_016218.6(POLK):c.1345G>A (p.Glu449Lys)Pathogenic
218222NM_016218.6(POLK):c.2033C>T (p.Ser678Phe)Pathogenic
218223NM_016218.6(POLK):c.2192T>A (p.Leu731His)Pathogenic
218224NM_016218.6(POLK):c.1582A>T (p.Ser528Cys)Pathogenic
218225NM_016218.6(POLK):c.1652A>T (p.Asp551Val)Pathogenic
218226NM_016218.6(POLK):c.1692G>A (p.Lys564=)Pathogenic
218227NM_016218.6(POLK):c.1741G>A (p.Asp581Asn)Pathogenic
218228NM_016218.6(POLK):c.1381A>G (p.Lys461Glu)Pathogenic
218229NM_016218.6(POLK):c.1460T>C (p.Ile487Thr)Pathogenic
218230NM_016218.6(POLK):c.464T>C (p.Phe155Ser)Pathogenic
218232NM_016218.6(POLK):c.461G>A (p.Gly154Glu)Pathogenic
218233NM_016218.6(POLK):c.512T>C (p.Phe171Ser)Pathogenic
218235NM_016218.6(POLK):c.2598T>G (p.Asp866Glu)Pathogenic

SpliceAI

5634 predictions. Top by Δscore:

VariantEffectΔscore
3:121432913:AATAC:Adonor_loss1.0000
3:121432914:ATAC:Adonor_loss1.0000
3:121432915:TA:Tdonor_loss1.0000
3:121432916:AC:Adonor_loss1.0000
3:121432917:C:CAdonor_loss1.0000
3:121433029:CAATC:Cacceptor_gain1.0000
3:121433034:CTA:Cacceptor_gain1.0000
3:121433037:C:CCacceptor_gain1.0000
3:121433040:CA:Cacceptor_gain1.0000
3:121433041:A:ACacceptor_gain1.0000
3:121433041:A:Cacceptor_gain1.0000
3:121439990:A:ACdonor_gain1.0000
3:121439991:C:CCdonor_gain1.0000
3:121440114:TCC:Tacceptor_gain1.0000
3:121440115:CC:Cacceptor_gain1.0000
3:121440115:CCC:Cacceptor_gain1.0000
3:121440116:CC:Cacceptor_gain1.0000
3:121440116:CCTA:Cacceptor_loss1.0000
3:121440117:C:CCacceptor_gain1.0000
3:121449310:ATTAC:Adonor_loss1.0000
3:121449311:TTAC:Tdonor_loss1.0000
3:121449312:TAC:Tdonor_loss1.0000
3:121449313:A:Tdonor_loss1.0000
3:121449314:CCTG:Cdonor_loss1.0000
3:121467639:CT:Cacceptor_gain1.0000
3:121467641:C:CCacceptor_gain1.0000
3:121468301:CTA:Cdonor_loss1.0000
3:121468303:A:ACdonor_gain1.0000
3:121468303:A:ATdonor_loss1.0000
3:121468303:ACCTG:Adonor_gain1.0000

AlphaMissense

5838 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
5:75569470:C:AA129D0.998
5:75573772:T:AV148D0.998
5:75573799:C:AA157D0.998
5:75581442:A:CS310R0.998
5:75581444:T:AS310R0.998
5:75581444:T:GS310R0.998
5:75593888:T:AV456D0.998
5:75547097:A:CK25N0.997
5:75547097:A:TK25N0.997
5:75573749:T:AN140K0.997
5:75573749:T:GN140K0.997
5:75573820:T:CL164P0.997
5:75581440:C:AA309D0.997
5:75583328:A:CS324R0.997
5:75583330:T:AS324R0.997
5:75583330:T:GS324R0.997
5:75593914:T:CF465L0.997
5:75593916:T:AF465L0.997
5:75593916:T:GF465L0.997
5:75594044:T:CL508P0.997
5:75569424:G:CA114P0.996
5:75573760:G:CR144T0.996
5:75573769:G:AG147D0.996
5:75581407:G:CR298P0.996
5:75581434:T:CL307P0.996
5:75583299:C:AA314D0.996
5:75593904:G:CK461N0.996
5:75593904:G:TK461N0.996
5:75547096:A:TK25I0.995
5:75569404:A:CD107A0.995

dbSNP variants (sampled 300 via entrez): RS1000005055 (5:75577076 A>T), RS1000017307 (5:75554545 G>C), RS1000071936 (5:75546782 C>T), RS1000151374 (5:75539648 G>A), RS1000174675 (5:75543932 C>A), RS1000192902 (5:75554776 G>A), RS1000228553 (5:75586486 A>T), RS1000245773 (5:75593627 T>G), RS1000275099 (5:75545511 A>G), RS1000387704 (5:75541310 A>AAAAAAC), RS1000465316 (5:75598751 T>C), RS1000522047 (5:75605832 G>A,C), RS1000541015 (5:75557923 G>T), RS1000578566 (5:75558467 C>G,T), RS1000702303 (5:75520481 A>C)

Disease associations

OMIM: gene MIM:605650 | disease phenotypes: MIM:616351

GenCC curated gene-disease

Mondo (3): prostate cancer (MONDO:0008315), intellectual disability, autosomal dominant 34 (MONDO:0014599), intellectual disability (MONDO:0001071)

Orphanet (2): Familial prostate cancer (Orphanet:1331), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

4 associations (top):

StudyTraitp-value
GCST007293_121Body fat distribution (arm fat ratio)2.000000e-10
GCST007293_23Body fat distribution (arm fat ratio)3.000000e-18
GCST007293_49Body fat distribution (arm fat ratio)1.000000e-14
GCST007295_54Body fat distribution (leg fat ratio)6.000000e-06

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004341body fat distribution

MeSH disease descriptors (2)

DescriptorNameTree numbers
D008607Intellectual DisabilityC10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539
D011471Prostatic NeoplasmsC04.588.945.440.770; C12.100.500.260.750; C12.100.500.565.625; C12.200.294.260.750; C12.200.294.565.625; C12.200.758.409.750; C12.900.619.750

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL5365 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 11,194 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL1014CANDESARTAN CILEXETIL411,194

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

8 potent at pChembl≥5 of 16 total, top 8 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
5.47IC503400nMMANOALIDE
5.25IC505600nMMANOALIDE
5.25IC505600nMCANDESARTAN CILEXETIL
5.25IC505600nMCHEMBL3960997
5.17IC506800nMCHEMBL1917196
5.09IC508100nMCHEMBL1917198
5.04IC509200nMCANDESARTAN CILEXETIL
5.01Ki9850nMPINOPHILIN A

PubChem BioAssay actives

8 with measured affinity, of 993 total; 6 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
(2R)-2-hydroxy-3-[(2R,6R)-6-hydroxy-5-[(E)-4-methyl-6-(2,6,6-trimethylcyclohexen-1-yl)hex-3-enyl]-3,6-dihydro-2H-pyran-2-yl]-2H-furan-5-one1315755: Inhibition of human DNA polymerase kappa (19 to 526 residues) preincubated for 15 mins followed by replicating non-damaged DNA substrate addition measured after 30 mins in presence of dCTP and dGTP by radioactive gel-based primer extension assayic503.4000uM
3-[3-tert-butylsulfanyl-1-[(4-chlorophenyl)methyl]-5-propan-2-yl-2,3-dihydro-1H-inden-2-yl]-2,2-dimethylpropanoic acid1315756: Inhibition of human DNA polymerase kappa (19 to 526 residues)-mediated TLS past acrolein derived ring-opened reduced form of gamma-HOPdG lesions preincubated for 15 mins followed by DNA substrate addition measured after 30 mins in presence of dCTP and dGTP by radioactive gel-based primer extension assayic505.6000uM
Candesartan Cilexetil1315756: Inhibition of human DNA polymerase kappa (19 to 526 residues)-mediated TLS past acrolein derived ring-opened reduced form of gamma-HOPdG lesions preincubated for 15 mins followed by DNA substrate addition measured after 30 mins in presence of dCTP and dGTP by radioactive gel-based primer extension assayic505.6000uM
(5,8-dioxonaphthalen-1-yl) dodecanoate627964: Inhibition of C-terminal His6-tagged human DNA polymerase kappa (amino acids 1 to 560) using poly(dA)/oligo(dT)18 (A/T = 2/1) and dTTP as the DNA template-primer and nucleotide substrate after 60 minsic506.8000uM
(5,8-dioxonaphthalen-1-yl) (Z)-octadec-9-enoate627964: Inhibition of C-terminal His6-tagged human DNA polymerase kappa (amino acids 1 to 560) using poly(dA)/oligo(dT)18 (A/T = 2/1) and dTTP as the DNA template-primer and nucleotide substrate after 60 minsic508.1000uM
[(7S,8S,8aS)-8-hydroxy-7-methyl-6-oxo-3-[(E)-prop-1-enyl]-8,8a-dihydro-1H-isochromen-7-yl] 2,4-dihydroxy-6-methylbenzoate654367: Competitive inhibition of human C-terminal-His6-tagged DNA polymerase kappa expressed in Escherichia coli using dTTP as substrate by Dixon plot analysiski9.8500uM

CTD chemical–gene interactions

42 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
2’-deoxycytidine 5’-triphosphateincreases reaction, increases stability, affects binding, decreases reaction2
Hydrogen Peroxidedecreases response to substance, increases expression, decreases reaction2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxideaffects expression, decreases reaction, increases mutagenesis2
N6-(2-hydroxy-3-buten-1-yl)-2’-deoxyadenosinedecreases activity1
N(2)-furfuryl-deoxyguanosineincreases reaction, increases stability1
N-(2’-deoxyguanosin-8-yl)-3-aminobenzanthroneaffects binding, decreases reaction1
TAK-243increases sumoylation1
triphenyl phosphateaffects expression1
diepoxybutaneaffects binding, decreases activity1
trichostatin Aaffects expression, decreases reaction1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
sodium arseniteincreases expression1
2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridineaffects activity1
2’-deoxyadenosineaffects binding, decreases activity1
MK-886decreases activity1
perfluorooctane sulfonic aciddecreases expression1
N-(deoxyguanosin-8-yl)-2-amino-1-methyl-6-phenylimidazo(4,5-b)pyridineaffects activity1
TDO inhibitor LM10decreases expression1
abrineincreases expression1
2-amino-1-methyl-6-phenolimidazo(4,5-b)pyridine-DNA adductaffects activity1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amidedecreases expression1
bisphenol Sincreases methylation1
jinfukangaffects cotreatment, decreases expression1
Irinotecandecreases expression1
Resveratrolaffects cotreatment, increases expression1
Benzeneaffects expression1
Cisplatinaffects cotreatment, decreases expression1
Clorgylineincreases expression1
Deoxyadenosinesdecreases activity1
Doxorubicindecreases expression1

ChEMBL screening assays

22 unique, capped per target: 20 binding, 2 functional

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL1023118BindingInhibition of human DNA polymerase kappaPenicilliols A and B, novel inhibitors specific to mammalian Y-family DNA polymerases. — Bioorg Med Chem
CHEMBL1794536FunctionalPUBCHEM_BIOASSAY: qHTS for Inhibitors of Polymerase Kappa. (Class of assay: confirmatory) [Related pubchem assays (depositor defined):AID588638]PubChem BioAssay data set

Cellosaurus cell lines

15 cell lines: 14 cancer cell line, 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_4W26293 TRE/FLAG-POLKTransformed cell lineFemale
CVCL_4W71POLK F171A MSH-Cancer cell lineMale
CVCL_4W72POLK KO hetero MSH-Cancer cell lineMale
CVCL_4W73POLK KO homo MSH-Cancer cell lineMale
CVCL_JG97POLK KO-POLH-/-Cancer cell lineMale
CVCL_JG98POLZ Y2779F-POLK+/-Cancer cell lineMale
CVCL_JH00POLK KO-CD compCancer cell lineMale
CVCL_JH01POLK CDCancer cell lineMale
CVCL_JH02POLK CD MSH-Cancer cell lineMale
CVCL_JH03POLK SG MSH-Cancer cell lineMale

Clinical trials (associated diseases)

300 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT00029224PHASE4COMPLETEDTreatment With Zoledronic Acid in Patients With Breast Cancer, Multiple Myeloma, and Prostate Cancer With Cancer Related Bone Lesions
NCT00035997PHASE4COMPLETEDOpen-label Trial on the Effect of I.V. Zoledronic Acid 4 mg on Bone Density in Hormone Sensitive Prostate Cancer Patients With Bone Metastasis
NCT00063609PHASE4COMPLETEDThe Effect of Zoledronic Acid on Bone Loss in Prostate Cancer Patients Undergoing Androgen Deprivation Therapy
NCT00103623PHASE4SUSPENDEDThe Plenaxis® Experience Study
NCT00106392PHASE4COMPLETEDA Safety and Efficacy Study of Prograf in the Prevention of Erectile Dysfunction After Radical Prostatectomy
NCT00185029PHASE4UNKNOWNMR-Lymphography and Lymph Node Staging in Prostate Cancer
NCT00199485PHASE4COMPLETEDAngelica Sinensis for the Treatment of Hot Flashes in Men Undergoing LHRH Therapy for Prostate Cancer
NCT00219219PHASE4COMPLETEDZoledronic Acid in the Prevention of Skeletal-related Events in Hormone Refractory and Hormone-sensitive Prostate Cancer Patients With Bone Metastases
NCT00219271PHASE4COMPLETEDEffect Of Zoledronic Acid On Circulating And Bone Marrow-Residing Prostate Cancer Cells In Patients With Clinically Localized Prostate Cancer
NCT00237146PHASE4COMPLETEDStudy to Evaluate Zoledronic Acid on Quality of Life and Skeletal-related Events as Adjuvant Treatment in Patients With Hormone-naïve Prostate Cancer and Bone Metastasis Who Have Undergone Orchiectomy
NCT00242554PHASE4COMPLETEDOpen-label Phase IV Clinical Trial to Evaluate the Safety and Tolerability of Zoledronic Acid in Patients With Prostate Cancer and Bone Metastases
NCT00280098PHASE4COMPLETEDDocetaxel in the Treatment of Hormone Refractory Prostate Cancer
NCT00293696PHASE4COMPLETEDCasodex/Zoladex Biomarkers in Localised Prostate Cancer
NCT00334139PHASE4COMPLETEDEffect of Zoledronic Acid on Bone Metabolism in Patients With Bone Metastasis and Prostate or Breast Cancer
NCT00375765PHASE4COMPLETEDEffects On Dihydrotestosterone Regulated Gene Expression In Benign Prostatic Hyperplasia Or Prostate Cancer
NCT00391690PHASE4COMPLETEDEvaluation of Bone Markers as Diagnostic Tools for Early Detection of Bone Metastases in Patients With High Risk Prostate Cancer
NCT00422708PHASE4COMPLETEDLocal Anesthesia for Prostate Biopsy
NCT00526331PHASE4COMPLETEDEvaluation of Arterial Pressure Based Cardiac Output for Goal-Directed Perioperative Therapy
NCT00590213PHASE4COMPLETEDCompare the Value of Prophylactic Versus Therapeutic Breast Radiotherapy in CASODEX
NCT00629330PHASE4TERMINATEDDissemination of Prostate Cancer Screening to PCP’s in African American Communities
NCT00771966PHASE4COMPLETEDRadical Prostatectomy and Perioperative Fluid Therapy
NCT00805701PHASE4COMPLETEDStudy Assessing The Efficacy And Safety Of Avodart (Dutasteride) At Improving Urinary Symptoms In Men With Prostate Cancer Who Are Undergoing Seed Implantation
NCT00859027PHASE4COMPLETEDEffect Of Risedronate On Bone Mass In Older Men Receiving Neoadjuvant Therapy For Prostate Cancer
NCT00906269PHASE4UNKNOWNCan Hyperbaric Oxygen Improve Erectile Function Following Surgery for Prostate Cancer
NCT00953277PHASE4COMPLETEDStudy of Nerve Reconstruction Using AVANCE in Subjects Who Undergo Robotic Assisted Prostatectomy for Treatment of Prostate Cancer
NCT00982800PHASE4COMPLETEDDoes Postoperative Gabapentin Reduce Pain, Opioid Consumption and Anxiety and Have a Positive Effect on Health Related Quality of Life After Radical Prostatectomy?
NCT01083199PHASE4COMPLETEDGlobal Performance Evaluation of the AMS CONTINUUM™ Device
NCT01136226PHASE4COMPLETEDEvaluate Recovery of Testosterone for Patients Using Eligard
NCT01161563PHASE4COMPLETEDRandomized Crossover Trial to Assess the Tolerability of Gonadotropin Releasing Hormone (GnRH) Analogue Administration
NCT01230905PHASE4COMPLETEDStudy to Monitor the Effects of Androgen Suppression Treatment on the Heart
NCT01296672PHASE4COMPLETED3 Month Finasteride Challenge Test Can Significantly Improve the Performance of Screening for Prostate Cancer
NCT01365143PHASE4TERMINATEDProspective Randomized Trial Comparing Robotic Versus Open Radical Prostatectomy
NCT01379742PHASE4UNKNOWNComparison of Between ThinSeed™ and OncoSeed™ for Permanent Prostate Brachytherapy
NCT01486563PHASE4COMPLETEDHydroxyethyl Starch and Renal Function After Radical Prostatectomy
NCT01511874PHASE4COMPLETEDEfficacy and Safety Study of ELIGARD 22.5mg With Prostate Cancer
NCT01512472PHASE4TERMINATEDFirmagon (Degarelix) Intermittent Therapy
NCT01547416PHASE4COMPLETEDThe Effect of Combined General/Epidural Anesthesia Versus General Anesthesia on Diaphragmatic Function
NCT01571544PHASE4COMPLETEDThe Use of Thermal Suits as Preventing Hypothermia During Surgery
NCT01581749PHASE4UNKNOWNEvaluation of Truebeam for Low-Intermediate Risk Prostate Cancer
NCT01649635PHASE4COMPLETEDStudy of Cabazitaxel Combined With Prednisone and Prophylaxis of Neutropenia Complications in the Treatment of Patients With Metastatic Castration-resistant Prostate Cancer