POGK

Summary

POGK (pogo transposable element derived with KRAB domain, HGNC:18800) is a protein-coding gene on chromosome 1q24.1, encoding Pogo transposable element with KRAB domain (Q9P215).

The exact function of the protein encoded by this gene is not known. However, this gene product contains a KRAB domain (which is involved in protein-protein interactions) at the N-terminus, and a transposase domain at the C-terminus, suggesting that it may belong to the family of DNA-mediated transposons in human.

Source: NCBI Gene 57645 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 67 total
• MANE Select transcript: NM_017542

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18800
Approved symbol	POGK
Name	pogo transposable element derived with KRAB domain
Location	1q24.1
Locus type	gene with protein product
Status	Approved
Aliases	KIAA15131, LST003, BASS2, KRBOX2
Ensembl gene	ENSG00000143157
Ensembl biotype	protein_coding
OMIM	620039
Entrez	57645

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 19 protein_coding

ENST00000367875, ENST00000367876, ENST00000449930, ENST00000898750, ENST00000898751, ENST00000898752, ENST00000898753, ENST00000898754, ENST00000928419, ENST00000928420, ENST00000928421, ENST00000928422, ENST00000928423, ENST00000928424, ENST00000928425, ENST00000928426, ENST00000928427, ENST00000972109, ENST00000972110

RefSeq mRNA: 2 — MANE Select: NM_017542 NM_001314014, NM_017542

CCDS: CCDS1254

Canonical transcript exons

ENST00000367876 — 6 exons

Exon	Start	End
ENSE00000958421	166846612	166846738
ENSE00000958422	166847494	166847592
ENSE00000958423	166848938	166850423
ENSE00000958424	166852585	166856359
ENSE00001445829	166839475	166839604
ENSE00003571197	166840955	166841088

Expression profiles

Bgee: expression breadth ubiquitous, 274 present calls, max score 92.92.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.8835 / max 475.9939, expressed in 1811 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
6412	26.2106	1808
6411	1.6728	1150

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 46	UBERON:0006483	92.92	gold quality
cortical plate	UBERON:0005343	92.83	gold quality
ganglionic eminence	UBERON:0004023	92.36	gold quality
medial globus pallidus	UBERON:0002477	92.12	gold quality
inferior vagus X ganglion	UBERON:0005363	91.74	gold quality
globus pallidus	UBERON:0001875	91.72	gold quality
subthalamic nucleus	UBERON:0001906	91.72	gold quality
corpus callosum	UBERON:0002336	91.57	gold quality
postcentral gyrus	UBERON:0002581	91.24	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	90.61	gold quality
parietal lobe	UBERON:0001872	90.53	gold quality
spinal cord	UBERON:0002240	90.53	gold quality
CA1 field of hippocampus	UBERON:0003881	90.32	gold quality
embryo	UBERON:0000922	90.01	gold quality
pigmented layer of retina	UBERON:0001782	89.87	gold quality
ventricular zone	UBERON:0003053	89.85	gold quality
adult organism	UBERON:0007023	89.70	gold quality
dorsal plus ventral thalamus	UBERON:0001897	89.60	gold quality
upper leg skin	UBERON:0004262	89.52	gold quality
orbitofrontal cortex	UBERON:0004167	89.22	gold quality
ventral tegmental area	UBERON:0002691	88.98	gold quality
lower lobe of lung	UBERON:0008949	88.76	gold quality
entorhinal cortex	UBERON:0002728	88.68	gold quality
pons	UBERON:0000988	88.54	gold quality
dorsal root ganglion	UBERON:0000044	88.42	gold quality
medulla oblongata	UBERON:0001896	88.37	gold quality
superior vestibular nucleus	UBERON:0007227	88.33	gold quality
amygdala	UBERON:0001876	88.22	gold quality
trigeminal ganglion	UBERON:0001675	88.15	gold quality
temporal lobe	UBERON:0001871	88.13	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	10.22
E-MTAB-7303	no	665.93

Regulation

Is transcription factor: yes

JASPAR motifs

Motif	Name	Family
MA2560.1	POGK	More than 3 adjacent zinc fingers

JASPAR matrix evidence (PMIDs): PMID:39605320

miRNA regulators (miRDB)

169 targeting POGK, 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-3924	100.00	72.09	2394
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-3134	100.00	66.43	777
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-4425	100.00	67.59	1049
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-6077	99.99	68.04	2299
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-8068	99.98	73.85	2376
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-8075	99.97	67.20	962
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-590-3P	99.96	74.34	6478
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-141-3P	99.94	72.79	2421
HSA-MIR-200A-3P	99.94	72.68	2420
HSA-MIR-539-5P	99.93	70.30	2855
HSA-MIR-22-3P	99.93	68.13	917
HSA-MIR-552-5P	99.93	68.56	1583
HSA-MIR-1-3P	99.93	72.35	1914
HSA-MIR-206	99.93	72.50	1893

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pogk	ENSMUSG00000040596
rattus_norvegicus	Pogk	ENSRNOG00000032058

Paralogs (12): CENPB (ENSG00000125817), TIGD7 (ENSG00000140993), POGZ (ENSG00000143442), TIGD6 (ENSG00000164296), TIGD4 (ENSG00000169989), TIGD3 (ENSG00000173825), TIGD5 (ENSG00000179886), TIGD2 (ENSG00000180346), JRKL (ENSG00000183340), TIGD1 (ENSG00000221944), JRK (ENSG00000234616), (ENSG00000293642)

Protein

Protein identifiers

Pogo transposable element with KRAB domain — Q9P215 (reviewed: Q9P215)

All UniProt accessions (2): Q9P215, Q5TIJ2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

RefSeq proteins (2): NP_001300943, NP_060012* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001909	KRAB	Domain
IPR003655	aKRAB	Domain
IPR004875	DDE_SF_endonuclease_dom	Domain
IPR006600	HTH_CenpB_DNA-bd_dom	Domain
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR018586	Brinker_DNA-bd	Domain
IPR036051	KRAB_dom_sf	Homologous_superfamily
IPR050863	CenT-Element_Derived	Family

Pfam: PF01352, PF03184, PF03221, PF09607

UniProt features (11 total): domain 3, region of interest 3, cross-link 2, chain 1, coiled-coil region 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9P215-F1	68.59	0.26

Functional residue map

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

Post-translational modifications (2): 384, 13

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 145 (showing top): CREL_01, ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN, USF_C, MYCMAX_01, USF_01, AAAGACA_MIR511, ACATTCC_MIR1_MIR206, BOYAULT_LIVER_CANCER_SUBCLASS_G123_UP, VDR_Q3, USF_02, GCM_CALM1, CCCNNGGGAR_OLF1_01, TGGAAA_NFAT_Q4_01, CAIRO_LIVER_DEVELOPMENT_UP, AACATTC_MIR4093P

GO Biological Process (1): regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (3): DNA binding (GO:0003677), nucleic acid binding (GO:0003676), protein binding (GO:0005515)

GO Cellular Component (2): nucleus (GO:0005634), nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
nucleic acid binding	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

672 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
POGK	TIGD5	Q53EQ6	572
POGK	TIGD7	Q6NT04	570
POGK	TIGD3	Q6B0B8	542
POGK	NAIF1	Q69YI7	537
POGK	PGBD2	Q6P3X8	524
POGK	ME2	P23368	517
POGK	LRRC52	Q8N7C0	513
POGK	ILDR2	Q71H61	511
POGK	EVI5L	Q96CN4	503
POGK	TMCO1	Q9UM00	503
POGK	ZBED8	Q8IZ13	498
POGK	JRKL	Q9Y4A0	496
POGK	PGBD1	Q96JS3	490
POGK	PGBD5	Q8N414	481
POGK	ILDR1	Q86SU0	480

IntAct

33 interactions, top by confidence:

A	B	Type	Score
ARPC1B	ARPC2	psi-mi:“MI:0914”(association)	0.920
RFXANK	RFXAP	psi-mi:“MI:0914”(association)	0.780
TCEAL1	CHEK1	psi-mi:“MI:0914”(association)	0.530
CCNDBP1	JUN	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF316	psi-mi:“MI:0914”(association)	0.530
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.530
POGK	HSP90AB1	psi-mi:“MI:0915”(physical association)	0.520
Trim28	FTH1	psi-mi:“MI:0915”(physical association)	0.400
UCHL3	POGK	psi-mi:“MI:0915”(physical association)	0.370
TRIM28	ZNF320	psi-mi:“MI:0914”(association)	0.350
TRIM11	BTN3A3	psi-mi:“MI:0914”(association)	0.350
WEE1	ZNF316	psi-mi:“MI:0914”(association)	0.350
EEF1AKMT2	IFT56	psi-mi:“MI:0914”(association)	0.350
S100P	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
PTGES3	SBNO1	psi-mi:“MI:0914”(association)	0.350
PRKY	METTL15	psi-mi:“MI:0914”(association)	0.350
TRIM11	RABGAP1L	psi-mi:“MI:0914”(association)	0.350
NAA11	DVL2	psi-mi:“MI:0914”(association)	0.350
ARL2BP	GNPAT	psi-mi:“MI:0914”(association)	0.350
NPAS1	CIBAR1	psi-mi:“MI:0914”(association)	0.350
PLEKHG7	MROH6	psi-mi:“MI:0914”(association)	0.350
UBXN6	ZSWIM8	psi-mi:“MI:0914”(association)	0.350
ZNF44	ZNF195	psi-mi:“MI:0914”(association)	0.350

BioGRID (43): POGK (Affinity Capture-MS), POGK (Affinity Capture-MS), POGK (Affinity Capture-MS), POGK (Affinity Capture-MS), POGK (Affinity Capture-MS), POGK (Affinity Capture-MS), POGK (Affinity Capture-MS), POGK (Affinity Capture-MS), POGK (Affinity Capture-MS), POGK (Affinity Capture-MS), POGK (Proximity Label-MS), POGK (Affinity Capture-MS), POGK (Affinity Capture-MS), POGK (Affinity Capture-MS), POGK (Affinity Capture-MS)

ESM2 similar proteins: A3KPE8, A4IFA3, A8MT19, B2RD01, B2RRL2, E1BB03, G5ED66, O14423, O16810, O60108, O75564, O96006, P20913, P20914, P39428, P49777, P54789, P55968, Q0E2Q3, Q0VBL1, Q13415, Q17RP2, Q28DG7, Q2HEW6, Q4V3E2, Q4W5G0, Q58DC8, Q5SMU7, Q5SVZ6, Q5U2X2, Q60976, Q6NT04, Q6R2W3, Q80TC5, Q80Z32, Q8BUZ3, Q8GT06, Q8GYE8, Q8IY51, Q8L727

Diamond homologs: A6NFI3, A6NM28, A6NNF4, A6QLU5, A8MQ14, A8MUV8, B4DU55, B4DX44, E9Q8G5, O60290, O75290, O75467, O94892, O95780, P0DPD5, P17014, P17031, P17032, P17097, P17098, P21506, P51523, P59923, Q02525, Q03936, Q05481, Q06732, Q08DG8, Q14586, Q14590, Q15928, Q16587, Q2M218, Q2TL60, Q3B7M4, Q3KQV3, Q3SXZ3, Q49AA0, Q4R6C2, Q4R8H9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	1
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

1523 predictions. Top by Δscore:

Variant	Effect	Δscore
1:166840954:GAGAT:G	acceptor_gain	1.0000
1:166841058:GAAA:G	donor_gain	1.0000
1:166841059:A:T	donor_gain	1.0000
1:166841062:G:GG	donor_gain	1.0000
1:166841084:GATGG:G	donor_gain	1.0000
1:166841087:GG:G	donor_gain	1.0000
1:166841088:GG:G	donor_gain	1.0000
1:166841091:AA:A	donor_loss	1.0000
1:166846699:G:GT	donor_gain	1.0000
1:166846699:G:T	donor_gain	1.0000
1:166846710:G:GT	donor_gain	1.0000
1:166858116:TACCT:T	donor_loss	1.0000
1:166858117:A:AC	donor_gain	1.0000
1:166858118:C:CC	donor_gain	1.0000
1:166858118:C:CT	donor_loss	1.0000
1:166858118:CCTG:C	donor_gain	1.0000
1:166858279:GGG:G	acceptor_gain	1.0000
1:166858282:C:CC	acceptor_gain	1.0000
1:166860181:TTTA:T	donor_loss	1.0000
1:166860182:TTAC:T	donor_loss	1.0000
1:166860183:TACC:T	donor_loss	1.0000
1:166860184:A:AT	donor_loss	1.0000
1:166860185:CCTTT:C	donor_gain	1.0000
1:166860211:C:CT	donor_gain	1.0000
1:166860212:T:TT	donor_gain	1.0000
1:166860333:TGATT:T	acceptor_gain	1.0000
1:166860334:GATT:G	acceptor_gain	1.0000
1:166860335:ATT:A	acceptor_gain	1.0000
1:166860336:TT:T	acceptor_gain	1.0000
1:166860336:TTC:T	acceptor_loss	1.0000

AlphaMissense

4041 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:166849189:T:C	F204L	1.000
1:166849190:T:C	F204S	1.000
1:166849191:C:A	F204L	1.000
1:166849191:C:G	F204L	1.000
1:166849192:A:C	K205Q	1.000
1:166849192:A:G	K205E	1.000
1:166849194:G:C	K205N	1.000
1:166849194:G:T	K205N	1.000
1:166849196:T:C	L206P	1.000
1:166849202:T:A	V208E	1.000
1:166849213:G:C	A212P	1.000
1:166849214:C:A	A212D	1.000
1:166849230:C:A	N217K	1.000
1:166849230:C:G	N217K	1.000
1:166849238:C:A	A220D	1.000
1:166849240:G:C	A221P	1.000
1:166849241:C:A	A221D	1.000
1:166849249:T:A	F224I	1.000
1:166849249:T:C	F224L	1.000
1:166849251:T:A	F224L	1.000
1:166849251:T:G	F224L	1.000
1:166849261:G:A	E228K	1.000
1:166849262:A:T	E228V	1.000
1:166849270:G:T	V231F	1.000
1:166849271:T:A	V231D	1.000
1:166849274:G:C	R232P	1.000
1:166849279:T:A	W234R	1.000
1:166849279:T:C	W234R	1.000
1:166849280:G:C	W234S	1.000
1:166849281:G:C	W234C	1.000

dbSNP variants (sampled 300 via entrez): RS1000034282 (1:166854383 T>C), RS1000298954 (1:166852598 G>C,T), RS1000345677 (1:166850236 G>A), RS1000845448 (1:166844644 C>G,T), RS1000875069 (1:166839169 A>G,T), RS1000947963 (1:166837655 G>A,C,T), RS1001074457 (1:166844985 G>A,T), RS1001226331 (1:166845535 G>A,T), RS1001274781 (1:166844387 G>C), RS1001302778 (1:166839269 C>A,T), RS1001332145 (1:166838988 G>A), RS1001594104 (1:166845929 C>T), RS1001626465 (1:166839623 GGGC>G,GGGCGGC,GGGCGGCGGC), RS1002002417 (1:166838697 T>A,C), RS1002233386 (1:166838282 C>T)

Disease associations

OMIM: gene MIM:620039 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST002681_2	Post-traumatic stress disorder	3.000000e-06
GCST010697_48	Cortical surface area (min-P)	3.000000e-13
GCST010698_42	Subcortical volume (min-P)	8.000000e-12
GCST010699_55	Brain morphology (min-P)	2.000000e-40
GCST010700_39	Cortical thickness (MOSTest)	4.000000e-08
GCST010701_100	Cortical surface area (MOSTest)	1.000000e-12
GCST010702_40	Subcortical volume (MOSTest)	2.000000e-10
GCST010703_26	Brain morphology (MOSTest)	5.000000e-09

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Cadmium Chloride	decreases expression, increases abundance, increases expression	3
Formaldehyde	decreases expression	2
Valproic Acid	affects expression, decreases expression	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
TAK-243	decreases sumoylation	1
triphenyl phosphate	affects expression	1
trichostatin A	affects expression	1
arsenite	decreases reaction, affects binding	1
sodium arsenite	decreases expression	1
cobaltous chloride	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
ICG 001	increases expression	1
Grape Seed Proanthocyanidins	affects cotreatment, decreases expression	1
(4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)	decreases expression	1
Resveratrol	affects cotreatment, increases expression	1
Sunitinib	increases expression	1
Cadmium	increases abundance, increases expression	1
Catechin	affects cotreatment, decreases expression	1
Ethyl Methanesulfonate	decreases expression	1
Lead	decreases expression	1
Mercury	affects expression	1
Methyl Methanesulfonate	decreases expression	1
Plant Extracts	affects cotreatment, increases expression	1
Rotenone	decreases expression	1
Silicon Dioxide	decreases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	increases expression, decreases methylation	1

Cellosaurus cell lines

5 cell lines: 5 cancer cell line

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

Cellosaurus	Name	Category	Sex
CVCL_B2BC	Abcam HeLa POGK KO	Cancer cell line	Female
CVCL_TE81	HAP1 POGK (-) 1	Cancer cell line	Male
CVCL_TE82	HAP1 POGK (-) 2	Cancer cell line	Male
CVCL_TE83	HAP1 POGK (-) 3	Cancer cell line	Male
CVCL_TE84	HAP1 POGK (-) 4	Cancer cell line	Male

Clinical trials (associated diseases)

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