POU3F1

Summary

POU3F1 (POU class 3 homeobox 1, HGNC:9214) is a protein-coding gene on chromosome 1p34.3, encoding POU domain, class 3, transcription factor 1 (Q03052). Transcription factor that binds to the octamer motif (5’-ATTTGCAT-3’).

Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in negative regulation of transcription by RNA polymerase II; positive regulation of DNA-templated transcription; and positive regulation of gene expression. Predicted to act upstream of or within keratinocyte differentiation; nervous system development; and positive regulation of transcription by RNA polymerase II. Located in nucleoplasm.

Source: NCBI Gene 5453 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 48 total
• Transcription factor: yes — 27 downstream targets (CollecTRI)
• MANE Select transcript: NM_002699

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9214
Approved symbol	POU3F1
Name	POU class 3 homeobox 1
Location	1p34.3
Locus type	gene with protein product
Status	Approved
Aliases	OCT6, SCIP
Ensembl gene	ENSG00000185668
Ensembl biotype	protein_coding
OMIM	602479
Entrez	5453

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000373012

RefSeq mRNA: 1 — MANE Select: NM_002699 NM_002699

CCDS: CCDS30679

Canonical transcript exons

ENST00000373012 — 1 exons

Exon	Start	End
ENSE00001459297	38043829	38046793

Expression profiles

Bgee: expression breadth ubiquitous, 135 present calls, max score 85.12.

FANTOM5 (CAGE): breadth broad, TPM avg 2.2456 / max 189.2221, expressed in 431 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
11835	2.2456	431

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
skin of abdomen	UBERON:0001416	85.12	gold quality
tibial nerve	UBERON:0001323	84.85	gold quality
skin of leg	UBERON:0001511	84.52	gold quality
zone of skin	UBERON:0000014	82.29	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.78	gold quality
upper arm skin	UBERON:0004263	79.00	silver quality
superficial temporal artery	UBERON:0001614	78.80	gold quality
CA1 field of hippocampus	UBERON:0003881	78.38	silver quality
gingiva	UBERON:0001828	77.09	silver quality
hair follicle	UBERON:0002073	76.74	gold quality
gingival epithelium	UBERON:0001949	76.50	silver quality
tongue squamous epithelium	UBERON:0006919	75.93	gold quality
Brodmann (1909) area 10	UBERON:0013541	75.78	gold quality
caudate nucleus	UBERON:0001873	75.56	gold quality
olfactory bulb	UBERON:0002264	75.13	gold quality
type B pancreatic cell	CL:0000169	74.68	gold quality
sural nerve	UBERON:0015488	74.61	gold quality
putamen	UBERON:0001874	74.39	gold quality
nucleus accumbens	UBERON:0001882	74.28	gold quality
epithelium of nasopharynx	UBERON:0001951	72.99	gold quality
mammalian vulva	UBERON:0000997	71.17	silver quality
cingulate cortex	UBERON:0003027	70.59	gold quality
anterior cingulate cortex	UBERON:0009835	70.40	gold quality
cortical plate	UBERON:0005343	70.13	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	69.55	gold quality
superior frontal gyrus	UBERON:0002661	69.45	gold quality
Ammon’s horn	UBERON:0001954	69.43	gold quality
postcentral gyrus	UBERON:0002581	69.42	silver quality
telencephalon	UBERON:0001893	69.17	gold quality
primary visual cortex	UBERON:0002436	68.95	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-10018	yes	226.44
E-ANND-3	no	2.28

Regulation

Is transcription factor: yes

Downstream targets (CollecTRI)

27 targets.

Target	Regulation
ADAM2
CCDC6
CHRNA2
CHRNA3
CNTF
CXCR4	Repression
DHH
EGR2	Activation
FABP7
GAL
GDNF
GNRH1	Unknown
IL6
IVL	Repression
KRT14	Repression
LORICRIN
MBP	Repression
MMP19	Repression
MMP9	Repression
MPZ	Repression
OXT
POU3F1
SOX2	Activation
SSTR1
TBXT
WNT1	Repression
ZFP42	Repression

JASPAR motifs

Motif	Name	Family
MA0786.1	POU3F1	POU domain factors
MA0786.2	POU3F1	POU domain factors

JASPAR matrix evidence (PMIDs): PMID:1361172

Upstream regulators (CollecTRI, top): POU3F1, STAT1

miRNA regulators (miRDB)

57 targeting POU3F1, 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-4668-3P	100.00	68.74	2635
HSA-MIR-4476	100.00	68.18	2030
HSA-MIR-6876-5P	100.00	67.68	2126
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-6755-5P	99.95	65.59	464
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-7-1-3P	99.91	71.53	4384
HSA-MIR-7-2-3P	99.91	71.40	4394
HSA-MIR-8063	99.91	69.76	3146
HSA-MIR-9902	99.89	69.15	2250
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-548D-3P	99.87	70.67	4362

Literature-anchored findings (GeneRIF, showing 4)

• Our results suggest that Tst-1 and Skn-1a regulate expression of MMPs in keratinocytes and effect both the expression and activation of these proteolytic enzymes. (PMID:17195013)
• Strict control of Pou3f1 transgene expression is critical to proper myelination, and factors responsible for Pouf31 downregulation during myelination may play important roles in the development of peripheral neuropathies. (PMID:17959798)
• CpG island hypermethylation contributes to down-regulation of Oct-6 mRNA expression in hepatocellular carcinoma. (PMID:21448695)
• Combined high OATP1A2/high OCT6 may be a potential predictor of response to anthracycline/taxane-based chemotherapy in breast cancer (PMID:24671357)

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	pou3f1	ENSDARG00000009823
danio_rerio	pou5f3	ENSDARG00000044774
mus_musculus	Pou3f1	ENSMUSG00000090125
rattus_norvegicus	Pou3f1	ENSRNOG00000047686
drosophila_melanogaster	acj6	FBGN0000028
drosophila_melanogaster	vvl	FBGN0086680
caenorhabditis_elegans		WBGENE00000441
caenorhabditis_elegans		WBGENE00006818

Paralogs (17): POU2F2 (ENSG00000028277), POU1F1 (ENSG00000064835), POU4F3 (ENSG00000091010), POU6F2 (ENSG00000106536), POU2F3 (ENSG00000137709), POU2F1 (ENSG00000143190), POU4F2 (ENSG00000151615), POU4F1 (ENSG00000152192), HDX (ENSG00000165259), POU6F1 (ENSG00000184271), POU3F2 (ENSG00000184486), POU3F4 (ENSG00000196767), POU3F3 (ENSG00000198914), CCDC160 (ENSG00000203952), POU5F1 (ENSG00000204531), POU5F1B (ENSG00000212993), POU5F2 (ENSG00000248483)

Protein

Protein identifiers

POU domain, class 3, transcription factor 1 — Q03052 (reviewed: Q03052)

Alternative names: Octamer-binding protein 6, Octamer-binding transcription factor 6, POU domain transcription factor SCIP

All UniProt accessions (1): Q03052

UniProt curated annotations — full annotation on UniProt →

Function. Transcription factor that binds to the octamer motif (5’-ATTTGCAT-3’). Acts as a transcriptional activator when binding cooperatively with SOX4, SOX11, or SOX12 to gene promoters. Acts as a transcriptional repressor of myelin-specific genes.

Subcellular location. Nucleus.

Tissue specificity. Expressed in embryonal stem cells and in the developing brain.

Similarity. Belongs to the POU transcription factor family. Class-3 subfamily.

RefSeq proteins (1): NP_002690* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000327	POU_dom	Domain
IPR001356	HD	Domain
IPR009057	Homeodomain-like_sf	Homologous_superfamily
IPR010982	Lambda_DNA-bd_dom_sf	Homologous_superfamily
IPR013847	POU	Domain
IPR016362	TF_POU_3	Family
IPR017970	Homeobox_CS	Conserved_site
IPR050255	POU_domain_TF	Family

Pfam: PF00046, PF00157

UniProt features (16 total): compositionally biased region 6, region of interest 5, sequence conflict 2, chain 1, domain 1, DNA-binding region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q03052-F1	60.82	0.24

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-9619665	EGR2 and SOX10-mediated initiation of Schwann cell myelination
R-HSA-9823739	Formation of the anterior neural plate
R-HSA-9832991	Formation of the posterior neural plate

MSigDB gene sets: 141 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, MULLIGHAN_NPM1_SIGNATURE_3_UP, BENPORATH_ES_WITH_H3K27ME3, GOBP_GLIAL_CELL_DEVELOPMENT, SCHLESINGER_METHYLATED_DE_NOVO_IN_CANCER, GOBP_NEUROGENESIS, GOBP_FOREBRAIN_DEVELOPMENT, SHEPARD_BMYB_MORPHOLINO_DN, RODRIGUES_NTN1_TARGETS_DN, GOBP_EPIDERMAL_CELL_DIFFERENTIATION, FOSTER_TOLERANT_MACROPHAGE_UP, LE_EGR2_TARGETS_UP, GOBP_ENSHEATHMENT_OF_NEURONS, GATA1_01, INGRAM_SHH_TARGETS_DN

GO Biological Process (12): regulation of transcription by RNA polymerase II (GO:0006357), axon ensheathment (GO:0008366), positive regulation of gene expression (GO:0010628), myelination in peripheral nervous system (GO:0022011), keratinocyte differentiation (GO:0030216), forebrain development (GO:0030900), positive regulation of DNA-templated transcription (GO:0045893), regulation of DNA-templated transcription (GO:0006355), brain development (GO:0007420), epidermis development (GO:0008544), Schwann cell development (GO:0014044), myelination (GO:0042552)

GO Molecular Function (6): RNA polymerase II cis-regulatory region sequence-specific DNA binding (GO:0000978), DNA-binding transcription factor activity, RNA polymerase II-specific (GO:0000981), DNA-binding transcription factor activity (GO:0003700), sequence-specific DNA binding (GO:0043565), sequence-specific double-stranded DNA binding (GO:1990837), DNA binding (GO:0003677)

GO Cellular Component (4): chromatin (GO:0000785), nucleus (GO:0005634), nucleoplasm (GO:0005654), transcription regulator complex (GO:0005667)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Gastrulation	2
Nervous system development	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	3
regulation of gene expression	2
DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
cellular anatomical structure	2
transcription by RNA polymerase II	1
ensheathment of neurons	1
gene expression	1
positive regulation of macromolecule biosynthetic process	1
Schwann cell development	1
peripheral nervous system axon ensheathment	1
myelination	1
epidermal cell differentiation	1
skin development	1
brain development	1
anatomical structure development	1
positive regulation of RNA biosynthetic process	1
regulation of RNA biosynthetic process	1
central nervous system development	1
animal organ development	1
head development	1
tissue development	1
Schwann cell differentiation	1
glial cell development	1
axon ensheathment	1
cis-regulatory region sequence-specific DNA binding	1
chromatin	1
DNA-binding transcription factor activity	1
regulation of transcription by RNA polymerase II	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
DNA binding	1
double-stranded DNA binding	1
sequence-specific DNA binding	1
nucleic acid binding	1
chromosome	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
protein-containing complex	1

Protein interactions and networks

STRING

1186 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
POU3F1	EGR2	P11161	758
POU3F1	RET	P07949	725
POU3F1	ZIC2	O95409	609
POU3F1	SOX10	P56693	590
POU3F1	OTX2	P32243	543
POU3F1	SOX2	P48431	511
POU3F1	NEUROD6	Q96NK8	475
POU3F1	RXRG	P48443	468
POU3F1	HOXC5	Q00444	463
POU3F1	BCL6B	Q8N143	454
POU3F1	FOS	P01100	451
POU3F1	ID4	P47928	449
POU3F1	LHX3	Q9UBR4	443
POU3F1	TAL1	P17542	442
POU3F1	SOX3	P35714	440

IntAct

8 interactions, top by confidence:

A	B	Type	Score
IFNA10	POU3F1	psi-mi:“MI:0915”(physical association)	0.370
IFNA4	POU3F1	psi-mi:“MI:0915”(physical association)	0.370
BMI1	MEIS3P1	psi-mi:“MI:0914”(association)	0.350
S100A2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
POU3F1	DUSP3	psi-mi:“MI:0914”(association)	0.350

BioGRID (15): HMGA1 (Reconstituted Complex), CCDC85A (Affinity Capture-MS), TTC7B (Affinity Capture-MS), TBC1D24 (Affinity Capture-MS), POU3F1 (Affinity Capture-MS), SSU72 (Affinity Capture-MS), EFHD1 (Affinity Capture-MS), DUSP3 (Affinity Capture-MS), EFR3A (Affinity Capture-MS), C17orf70 (Affinity Capture-MS), AIDA (Affinity Capture-MS), PDZD11 (Affinity Capture-MS), PAK1 (Affinity Capture-MS), POU3F1 (Affinity Capture-MS), POU3F1 (Affinity Capture-MS)

ESM2 similar proteins: A2WY46, A6BLW4, B8A9B2, G0SB31, G4MRQ6, G4N3L5, M2TF54, O54772, O65001, O70132, P17208, P20264, P20265, P20266, P20267, P21952, P25209, P31360, P31361, P53784, P56222, Q01851, Q02516, Q03052, Q0JGS5, Q13164, Q60764, Q60EQ4, Q63262, Q655V5, Q69J40, Q69TW5, Q6EU10, Q75IZ7, Q8L4B2, Q8LCG7, Q8LH59, Q8QZW2, Q92925, Q960X8

Diamond homologs: A0A1L8FFY5, A1L0Z1, A7Y7W2, B3DM23, B3DM25, B7ZQA9, D3ZTL1, G3V7L5, O97552, P09086, P10036, P10037, P13528, P14859, P15143, P16143, P16241, P17208, P20263, P20264, P20265, P20266, P20267, P20268, P20912, P20913, P20914, P21952, P24350, P25425, P28069, P31360, P31361, P31362, P31363, P31364, P31365, P31367, P31368, P31369

SIGNOR signaling

2 interactions.

A	Effect	B	Mechanism
HMGA1	“up-regulates activity”	POU3F1	binding
HMGB2	“up-regulates activity”	POU3F1	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	46
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

26 predictions. Top by Δscore:

Variant	Effect	Δscore
1:38044550:CGGA:C	acceptor_gain	0.6400
1:38044549:T:TG	acceptor_gain	0.5800
1:38046601:T:TA	donor_gain	0.4600
1:38045892:G:GT	acceptor_gain	0.4200
1:38045893:T:TT	acceptor_gain	0.4200
1:38044553:A:C	acceptor_gain	0.4100
1:38044550:C:A	acceptor_gain	0.3400
1:38046725:A:AC	donor_gain	0.3400
1:38046726:C:CC	donor_gain	0.3400
1:38044553:A:AC	acceptor_gain	0.3200
1:38046414:T:TA	donor_gain	0.2900
1:38046593:TCTGC:T	donor_gain	0.2900
1:38046590:G:C	donor_gain	0.2800
1:38044551:G:T	acceptor_gain	0.2700
1:38046465:G:A	donor_gain	0.2400
1:38046460:G:A	donor_gain	0.2300
1:38044042:C:CT	acceptor_gain	0.2200
1:38045023:CTGCG:C	donor_gain	0.2200
1:38045024:TGCGT:T	donor_gain	0.2200
1:38045027:G:C	donor_gain	0.2200
1:38046593:T:TA	donor_gain	0.2200
1:38045851:GCCTC:G	acceptor_gain	0.2100
1:38045874:C:CC	acceptor_gain	0.2100
1:38045894:A:AT	acceptor_gain	0.2100
1:38044559:C:CT	acceptor_gain	0.2000
1:38046406:TGGAA:T	donor_gain	0.2000

AlphaMissense

2884 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:38045558:G:A	R396C	1.000
1:38045558:G:T	R396S	1.000
1:38045559:C:A	K395N	1.000
1:38045559:C:G	K395N	1.000
1:38045561:T:C	K395E	1.000
1:38045565:C:A	K393N	1.000
1:38045565:C:G	K393N	1.000
1:38045566:T:A	K393M	1.000
1:38045567:T:C	K393E	1.000
1:38045567:T:G	K393Q	1.000
1:38045568:C:A	Q392H	1.000
1:38045568:C:G	Q392H	1.000
1:38045569:T:G	Q392P	1.000
1:38045570:G:T	Q392K	1.000
1:38045572:C:G	R391P	1.000
1:38045572:C:T	R391Q	1.000
1:38045573:G:A	R391W	1.000
1:38045573:G:C	R391G	1.000
1:38045575:C:G	R390P	1.000
1:38045576:G:A	R390W	1.000
1:38045576:G:C	R390G	1.000
1:38045577:G:C	N389K	1.000
1:38045577:G:T	N389K	1.000
1:38045578:T:A	N389I	1.000
1:38045578:T:G	N389T	1.000
1:38045579:T:A	N389Y	1.000
1:38045579:T:C	N389D	1.000
1:38045579:T:G	N389H	1.000
1:38045580:G:C	C388W	1.000
1:38045581:C:A	C388F	1.000

dbSNP variants (sampled 300 via entrez): RS1000716740 (1:38043738 T>A,C), RS1000811573 (1:38043484 T>A,G), RS1001456540 (1:38046914 C>T), RS1001537856 (1:38047511 C>T), RS1001807722 (1:38043369 T>C), RS1002105631 (1:38046879 C>T), RS1002822361 (1:38047874 G>T), RS1003520027 (1:38045145 G>A,T), RS1003947027 (1:38047604 C>A), RS1005128778 (1:38044525 C>T), RS1006225419 (1:38044265 C>G,T), RS1006772663 (1:38043774 G>A,C), RS1006777780 (1:38048685 G>A), RS1006844825 (1:38044157 A>G), RS1008419779 (1:38047419 G>A,C,T)

Disease associations

OMIM: gene MIM:602479 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001524_28	Visceral adipose tissue/subcutaneous adipose tissue ratio	8.000000e-06
GCST001754_3	Waist-to-hip circumference ratio (ever vs never smoking interaction)	3.000000e-06
GCST005568_44	Rheumatoid arthritis (ACPA-positive)	2.000000e-08
GCST005569_18	Rheumatoid arthritis	1.000000e-07
GCST006048_36	Rheumatoid arthritis (ACPA-positive)	2.000000e-08
GCST012490_448	Femur bone mineral density x serum urate levels interaction	2.000000e-10

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004767	visceral:subcutaneous adipose tissue ratio
EFO:0004343	waist-hip ratio
EFO:0004531	urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases methylation	7
trichostatin A	decreases expression, affects cotreatment	3
sodium arsenite	decreases expression, increases expression	2
mercuric bromide	affects cotreatment, decreases expression	2
entinostat	decreases expression, affects cotreatment	2
Vorinostat	affects cotreatment, decreases expression	2
Panobinostat	affects cotreatment, decreases expression	2
Benzo(a)pyrene	increases methylation, affects methylation, increases expression	2
Lead	affects expression, decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tretinoin	affects expression, decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
aristolochic acid I	increases expression	1
GSK-J4	increases expression	1
TL8-506	increases expression, affects cotreatment	1
methylmercuric chloride	increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
perfluorooctanoic acid	affects cotreatment, decreases expression	1
ferrous chloride	decreases expression	1
perfluorooctane sulfonic acid	affects cotreatment, decreases expression	1
CD 437	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
perfluorohexanesulfonic acid	affects cotreatment, decreases expression	1
3-(4’-hydroxy-3’-adamantylbiphenyl-4-yl)acrylic acid	decreases expression	1
nutlin 3	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
licochalcone B	increases expression	1
jinfukang	affects cotreatment, increases expression	1
Calcitriol	increases expression	1
Cisplatin	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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