PDIK1L

Summary

PDIK1L (PDLIM1 interacting kinase 1 like, HGNC:18981) is a protein-coding gene on chromosome 1p36.11, encoding Serine/threonine-protein kinase PDIK1L (Q8N165).

Predicted to enable protein kinase activity. Predicted to be involved in negative regulation of G2/M transition of mitotic cell cycle and negative regulation of G2/MI transition of meiotic cell cycle. Located in nucleoplasm.

Source: NCBI Gene 149420 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 21 total
• MANE Select transcript: NM_152835

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18981
Approved symbol	PDIK1L
Name	PDLIM1 interacting kinase 1 like
Location	1p36.11
Locus type	gene with protein product
Status	Approved
Aliases	CLIK1L, STK35L2
Ensembl gene	ENSG00000175087
Ensembl biotype	protein_coding
OMIM	610785
Entrez	149420

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 9 protein_coding

ENST00000374269, ENST00000374271, ENST00000444713, ENST00000619836, ENST00000866849, ENST00000866850, ENST00000866851, ENST00000866852, ENST00000941975

RefSeq mRNA: 3 — MANE Select: NM_152835 NM_001243532, NM_001243533, NM_152835

CCDS: CCDS274

Canonical transcript exons

ENST00000374269 — 3 exons

Exon	Start	End
ENSE00001462969	26121837	26125555
ENSE00001462970	26111824	26111915
ENSE00001462972	26114292	26114593

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 93.66.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.9754 / max 72.9470, expressed in 1590 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
1558	5.2215	1448
1556	0.9914	607
1557	0.7626	408

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cortical plate	UBERON:0005343	93.66	gold quality
palpebral conjunctiva	UBERON:0001812	90.67	gold quality
esophagus squamous epithelium	UBERON:0006920	89.36	gold quality
epithelium of nasopharynx	UBERON:0001951	86.54	gold quality
epithelial cell of pancreas	CL:0000083	86.24	silver quality
ganglionic eminence	UBERON:0004023	86.20	gold quality
gingival epithelium	UBERON:0001949	85.88	gold quality
secondary oocyte	CL:0000655	85.85	gold quality
germinal epithelium of ovary	UBERON:0001304	85.60	gold quality
upper arm skin	UBERON:0004263	85.58	silver quality
gingiva	UBERON:0001828	85.05	gold quality
bone marrow	UBERON:0002371	84.10	gold quality
oocyte	CL:0000023	83.75	gold quality
ventricular zone	UBERON:0003053	83.18	gold quality
jejunal mucosa	UBERON:0000399	83.11	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.03	gold quality
visceral pleura	UBERON:0002401	82.72	gold quality
trabecular bone tissue	UBERON:0002483	82.69	gold quality
bone marrow cell	CL:0002092	82.56	gold quality
bronchial epithelial cell	CL:0002328	81.59	gold quality
bronchus	UBERON:0002185	80.95	gold quality
calcaneal tendon	UBERON:0003701	80.86	gold quality
pigmented layer of retina	UBERON:0001782	80.69	gold quality
islet of Langerhans	UBERON:0000006	80.68	gold quality
amniotic fluid	UBERON:0000173	80.65	gold quality
nasal cavity mucosa	UBERON:0001826	80.58	gold quality
mucosa of paranasal sinus	UBERON:0005030	80.48	gold quality
oral cavity	UBERON:0000167	79.90	gold quality
vastus lateralis	UBERON:0001379	79.66	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	79.53	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.15

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): MAZ, MYC, NFKB, TAL1

miRNA regulators (miRDB)

210 targeting PDIK1L, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-188-3P	100.00	68.76	1240
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4776-3P	100.00	68.73	1340
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548AW	99.99	72.57	3559
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-103A-3P	99.98	69.14	1595

Literature-anchored findings (GeneRIF, showing 1)

• SCP4-STK35/PDIK1L complex is a dual phospho-catalytic signaling dependency in acute myeloid leukemia. (PMID:35021089)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	pdik1l	ENSDARG00000056509
mus_musculus	Pdik1l	ENSMUSG00000050890
rattus_norvegicus	Pdik1l	ENSRNOG00000016536
drosophila_melanogaster	Wee1	FBGN0011737

Paralogs (8): EIF2AK2 (ENSG00000055332), EIF2AK1 (ENSG00000086232), STK35 (ENSG00000125834), PKMYT1 (ENSG00000127564), EIF2AK4 (ENSG00000128829), WEE1 (ENSG00000166483), EIF2AK3 (ENSG00000172071), WEE2 (ENSG00000214102)

Protein

Protein identifiers

Serine/threonine-protein kinase PDIK1L — Q8N165 (reviewed: Q8N165)

Alternative names: PDLIM1-interacting kinase 1-like

All UniProt accessions (2): Q8N165, X6RHF8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Tissue specificity. Expressed in liver, kidney, pancreas, spleen, thymus and prostate.

Similarity. Belongs to the protein kinase superfamily. Ser/Thr protein kinase family.

RefSeq proteins (3): NP_001230461, NP_001230462, NP_690048* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000719	Prot_kinase_dom	Domain
IPR008271	Ser/Thr_kinase_AS	Active_site
IPR011009	Kinase-like_dom_sf	Homologous_superfamily
IPR017441	Protein_kinase_ATP_BS	Binding_site
IPR050339	CC_SR_Kinase	Family

Pfam: PF00069

Catalyzed reactions (Rhea), 2 shown:

• L-seryl-[protein] + ATP = O-phospho-L-seryl-[protein] + ADP + H(+) (RHEA:17989)
• L-threonyl-[protein] + ATP = O-phospho-L-threonyl-[protein] + ADP + H(+) (RHEA:46608)

UniProt features (5 total): binding site 2, chain 1, domain 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N165-F1	86.13	0.63

Functional residue map

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

Catalytic / active sites (1): 164 (proton acceptor)

Ligand- & substrate-binding residues (2): 14–22; 37

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 228 (showing top): TGGTGCT_MIR29A_MIR29B_MIR29C, GOBP_NEGATIVE_REGULATION_OF_REPRODUCTIVE_PROCESS, TGCTGCT_MIR15A_MIR16_MIR15B_MIR195_MIR424_MIR497, GGGNRMNNYCAT_UNKNOWN, SP3_Q3, GOBP_CELL_CYCLE_PHASE_TRANSITION, CACCAGC_MIR138, GOBP_REGULATION_OF_MEIOTIC_CELL_CYCLE, SP1_Q2_01, FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_DN, GOBP_REGULATION_OF_CELL_CYCLE_G2_M_PHASE_TRANSITION, GTGCCTT_MIR506, GOBP_NEGATIVE_REGULATION_OF_MEIOTIC_CELL_CYCLE, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE_PROCESS, GOBP_NEGATIVE_REGULATION_OF_CELL_CYCLE

GO Biological Process (3): negative regulation of G2/M transition of mitotic cell cycle (GO:0010972), negative regulation of G2/MI transition of meiotic cell cycle (GO:0110031), protein phosphorylation (GO:0006468)

GO Molecular Function (8): protein kinase activity (GO:0004672), protein serine/threonine kinase activity (GO:0004674), ATP binding (GO:0005524), protein serine kinase activity (GO:0106310), nucleotide binding (GO:0000166), protein binding (GO:0005515), kinase activity (GO:0016301), transferase activity (GO:0016740)

GO Cellular Component (3): nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
negative regulation of cell cycle G2/M phase transition	2
protein kinase activity	2
cellular anatomical structure	2
G2/M transition of mitotic cell cycle	1
regulation of G2/M transition of mitotic cell cycle	1
negative regulation of mitotic cell cycle phase transition	1
G2/MI transition of meiotic cell cycle	1
regulation of G2/MI transition of meiotic cell cycle	1
negative regulation of meiotic cell cycle phase transition	1
phosphorylation	1
protein modification process	1
kinase activity	1
phosphotransferase activity, alcohol group as acceptor	1
catalytic activity, acting on a protein	1
adenyl ribonucleotide binding	1
purine ribonucleoside triphosphate binding	1
nucleoside phosphate binding	1
heterocyclic compound binding	1
binding	1
transferase activity, transferring phosphorus-containing groups	1
catalytic activity	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
intracellular anatomical structure	1

Protein interactions and networks

STRING

1136 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PDIK1L	GUCY2F	P51841	744
PDIK1L	PTPRK	Q15262	740
PDIK1L	GORAB	Q5T7V8	644
PDIK1L	RSPO2	Q6UXX9	560
PDIK1L	KRT71	Q3SY84	547
PDIK1L	MAP3K21	Q5TCX8	534
PDIK1L	MYLK2	Q9H1R3	518
PDIK1L	CDC7	O00311	514
PDIK1L	FGF5	P12034	475
PDIK1L	TPD52L3	Q96J77	453
PDIK1L	TXK	P42681	450
PDIK1L	WDSUB1	Q8N9V3	446
PDIK1L	MANEAL	Q5VSG8	434
PDIK1L	FAM110D	Q8TAY7	423
PDIK1L	SYDE1	Q6ZW31	406

IntAct

37 interactions, top by confidence:

A	B	Type	Score
C1orf174	PDIK1L	psi-mi:“MI:0915”(physical association)	0.900
CTDSPL2	PDIK1L	psi-mi:“MI:0915”(physical association)	0.840
PDIK1L	CTDSPL2	psi-mi:“MI:0914”(association)	0.840
PDIK1L	HSP90AB1	psi-mi:“MI:0915”(physical association)	0.740
PDIK1L	CDC37	psi-mi:“MI:0915”(physical association)	0.740
FKBP5	PDIK1L	psi-mi:“MI:0914”(association)	0.640
DAZAP2	PDIK1L	psi-mi:“MI:0915”(physical association)	0.560
C1orf174	AHCYL1	psi-mi:“MI:0914”(association)	0.530
PDIK1L	HSP90AA1	psi-mi:“MI:0914”(association)	0.530
PDIK1L	HSP90AA1	psi-mi:“MI:0914”(association)	0.350
PDIK1L	CSTB	psi-mi:“MI:0914”(association)	0.350
C1orf174	H2AC11	psi-mi:“MI:0914”(association)	0.350
CTDSPL2	PDIK1L	psi-mi:“MI:0915”(physical association)	0.000
PDIK1L	C1orf174	psi-mi:“MI:0915”(physical association)	0.000
PDIK1L	DAZAP2	psi-mi:“MI:0915”(physical association)	0.000
PDIK1L	CTDSPL2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (41): C1orf174 (Two-hybrid), CTDSPL2 (Affinity Capture-MS), C1orf174 (Affinity Capture-MS), HSP90AB4P (Affinity Capture-MS), HSP90AA5P (Affinity Capture-MS), FKBP5 (Affinity Capture-MS), SRC (Affinity Capture-MS), CDC37 (Affinity Capture-MS), HSP90AA1 (Affinity Capture-MS), HSP90AB1 (Affinity Capture-MS), PDIK1L (Two-hybrid), DAZAP2 (Two-hybrid), C1orf174 (Two-hybrid), PDIK1L (Affinity Capture-MS), CDC37 (Affinity Capture-MS)

ESM2 similar proteins: A6QLK5, A6ZKI3, D2HBJ8, O15519, O94955, O95751, P0CW24, P10272, Q0V9G5, Q17QF6, Q17RB0, Q1JQ94, Q2TBA3, Q5RD56, Q5RER6, Q5XGZ2, Q63053, Q6NTR6, Q6P5G6, Q6SEH4, Q6SEH5, Q70Z35, Q7JV70, Q7K1U0, Q7LC44, Q7TPY9, Q86TG7, Q8AWC3, Q8C1C8, Q8CA95, Q8N165, Q8N635, Q8ND90, Q8QZR7, Q8TCU6, Q8VHZ4, Q8WNV3, Q96PV4, Q9BWD3, Q9BYG7

Diamond homologs: A0A1B5KW97, A0A5B9GBF0, A0A8I5ZNK2, A1CPG7, A1D2C9, A1IVT7, A2QRF6, A2X6X1, A2YNT8, A3EZ53, A3EZ54, A3EZ55, A3LN91, A8XSC1, B0XR80, B1H3E1, B5DE93, D2H526, D3ZHP7, D3ZSZ3, E1BB50, E1BB52, E1BMN8, E2QWQ2, G1XJZ4, M1T7M3, O54949, O59853, O59854, O61267, O93982, O95747, P0C431, P0CP68, P0CP69, P32485, P32490, P36615, P41808, P43568

SIGNOR signaling

3 interactions.

A	Effect	B	Mechanism
PDIK1L	“form complex”	STK35/PDIK1L	binding
CTDSPL2	“up-regulates quantity by stabilization”	PDIK1L	dephosphorylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	17
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

596 predictions. Top by Δscore:

Variant	Effect	Δscore
1:26121835:A:AG	acceptor_gain	1.0000
1:26121836:G:GT	acceptor_gain	1.0000
1:26121836:GC:G	acceptor_gain	1.0000
1:26121836:GCTT:G	acceptor_gain	1.0000
1:26111416:GCTCG:G	donor_gain	0.9900
1:26112569:A:T	donor_gain	0.9900
1:26112614:A:T	donor_gain	0.9900
1:26120546:ACC:A	donor_gain	0.9900
1:26121835:AGCTT:A	acceptor_gain	0.9900
1:26121836:GCT:G	acceptor_gain	0.9900
1:26121836:GCTTG:G	acceptor_gain	0.9900
1:26111420:GGTA:G	donor_loss	0.9800
1:26111421:G:GA	donor_loss	0.9800
1:26111422:T:A	donor_loss	0.9800
1:26112613:G:GT	donor_gain	0.9800
1:26120541:A:T	donor_gain	0.9800
1:26121832:T:A	acceptor_gain	0.9800
1:26111421:G:GG	donor_gain	0.9700
1:26114912:A:AG	acceptor_gain	0.9700
1:26120410:T:A	acceptor_gain	0.9600
1:26121831:TTGTA:T	acceptor_gain	0.9500
1:26121832:TGTA:T	acceptor_gain	0.9500
1:26121833:GTA:G	acceptor_gain	0.9500
1:26121834:TA:T	acceptor_gain	0.9500
1:26121835:A:AC	acceptor_gain	0.9500
1:26121836:G:T	acceptor_gain	0.9500
1:26112628:GAAAT:G	donor_gain	0.9400
1:26112629:A:T	donor_gain	0.9400
1:26114290:A:AG	acceptor_gain	0.9400
1:26114291:G:GG	acceptor_gain	0.9400

AlphaMissense

2267 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:26114412:C:A	A35E	1.000
1:26114417:A:G	K37E	1.000
1:26114419:G:C	K37N	1.000
1:26114419:G:T	K37N	1.000
1:26121994:T:C	L148P	1.000
1:26122011:T:C	F154L	1.000
1:26122013:C:A	F154L	1.000
1:26122013:C:G	F154L	1.000
1:26122039:G:C	R163P	1.000
1:26122042:A:C	D164A	1.000
1:26122042:A:G	D164G	1.000
1:26122042:A:T	D164V	1.000
1:26122043:T:A	D164E	1.000
1:26122043:T:G	D164E	1.000
1:26122045:T:A	L165H	1.000
1:26122045:T:C	L165P	1.000
1:26122047:A:G	K166E	1.000
1:26122049:G:C	K166N	1.000
1:26122049:G:T	K166N	1.000
1:26122056:A:G	N169D	1.000
1:26122058:C:A	N169K	1.000
1:26122058:C:G	N169K	1.000
1:26122063:T:C	L171P	1.000
1:26122119:G:C	D190H	1.000
1:26122120:A:C	D190A	1.000
1:26122120:A:G	D190G	1.000
1:26122120:A:T	D190V	1.000
1:26122121:T:A	D190E	1.000
1:26122121:T:G	D190E	1.000
1:26122123:T:C	F191S	1.000

dbSNP variants (sampled 300 via entrez): RS1000277872 (1:26123227 G>A), RS1000338922 (1:26116598 T>G), RS1000392627 (1:26116295 A>G), RS1000851931 (1:26120825 G>A,T), RS1000880065 (1:26121372 A>G), RS1001287032 (1:26109267 C>A,T), RS1001342725 (1:26125632 T>A), RS1001343900 (1:26115246 T>C), RS1001389333 (1:26121127 G>A), RS1001478217 (1:26126027 G>A), RS1001504817 (1:26118086 T>C), RS1001554439 (1:26111219 A>G), RS1001634968 (1:26109551 TG>T), RS1001909360 (1:26112541 A>T), RS1001933460 (1:26119731 T>C)

Disease associations

OMIM: gene MIM:610785 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008476_21	Emphysema annual change measurement in smokers (percent low attenuation area)	8.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0007626	emphysema imaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

GtoPdb / IUPHAR curated pharmacology

(IUPHAR/BPS Guide to Pharmacology — expert-curated)

Target class: enzyme — NKF4 family

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, affects expression	5
Air Pollutants	increases abundance, increases expression, affects expression	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	affects binding, decreases expression, increases activity	1
bisphenol A	decreases methylation, affects cotreatment	1
sodium arsenite	increases expression	1
pentanal	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
ICG 001	increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Atrazine	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Clorgyline	increases expression	1
Formaldehyde	decreases expression	1
Ozone	affects expression, increases abundance	1
Quercetin	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Tunicamycin	increases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	decreases expression	1
Okadaic Acid	decreases expression	1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_TC75	HAP1 PDIK1L (-) 1	Cancer cell line	Male
CVCL_TC76	HAP1 PDIK1L (-) 2	Cancer cell line	Male
CVCL_TC77	HAP1 PDIK1L (-) 3	Cancer cell line	Male

Clinical trials (associated diseases)

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