FOXL3

gene

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Summary

FOXL3 (forkhead box L3, HGNC:54201) is a protein-coding gene on chromosome 7p22.3, encoding Forkhead box protein L3 (A0A1W2PRP0). Probable transcriptional regulator.

Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in anatomical structure morphogenesis; cell differentiation; and regulation of transcription by RNA polymerase II. Predicted to be located in nucleus.

Source: NCBI Gene 116033993 — RefSeq curated summary.

At a glance

Clinical variants (ClinVar): 4 total
MANE Select transcript: NM_001374838

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:54201
Approved symbol	FOXL3
Name	forkhead box L3
Location	7p22.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000248767
Ensembl biotype	protein_coding
Entrez	116033993

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 protein_coding, 1 nonsense_mediated_decay

ENST00000506382, ENST00000510017

RefSeq mRNA: 1 — MANE Select: NM_001374838 NM_001374838

CCDS: CCDS94042

Canonical transcript exons

ENST00000506382 — 3 exons

Exon	Start	End
ENSE00002086976	290653	290821
ENSE00003809049	290170	290276
ENSE00003809458	291063	291488

Expression profiles

Bgee: expression breadth broad, 36 present calls, max score 85.67.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	85.67	gold quality
left testis	UBERON:0004533	85.58	gold quality
testis	UBERON:0000473	84.82	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	54.07	gold quality
rectum	UBERON:0001052	46.49	gold quality
sural nerve	UBERON:0015488	45.31	gold quality
smooth muscle tissue	UBERON:0001135	42.67	gold quality
colonic epithelium	UBERON:0000397	42.56	gold quality
cortical plate	UBERON:0005343	41.05	gold quality
bone marrow cell	CL:0002092	40.13	silver quality
muscle tissue	UBERON:0002385	38.66	gold quality
skeletal muscle tissue	UBERON:0001134	37.86	silver quality
ganglionic eminence	UBERON:0004023	37.65	silver quality
ventricular zone	UBERON:0003053	36.48	gold quality
transverse colon	UBERON:0001157	35.64	gold quality
bone marrow	UBERON:0002371	33.77	silver quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
gastrocnemius	UBERON:0001388	31.39	gold quality
muscle of leg	UBERON:0001383	31.31	gold quality
colon	UBERON:0001155	31.02	gold quality
intestine	UBERON:0000160	29.98	gold quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
right coronary artery	UBERON:0001625	29.75	silver quality
right lobe of liver	UBERON:0001114	29.21	silver quality
tonsil	UBERON:0002372	28.86	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
leukocyte	CL:0000738	27.47	gold quality
monocyte	CL:0000576	27.45	gold quality
islet of Langerhans	UBERON:0000006	26.55	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.65

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	foxl3	ENSDARG00000086055
mus_musculus	Foxl3	ENSMUSG00000094504
rattus_norvegicus	Foxl3	ENSRNOG00000039296

Paralogs (41): FOXP3 (ENSG00000049768), FOXC1 (ENSG00000054598), FOXJ2 (ENSG00000065970), FOXF1 (ENSG00000103241), FOXN1 (ENSG00000109101), FOXM1 (ENSG00000111206), FOXP1 (ENSG00000114861), FOXO3 (ENSG00000118689), FOXA2 (ENSG00000125798), FOXA1 (ENSG00000129514), FOXJ1 (ENSG00000129654), FOXK2 (ENSG00000141568), FOXO1 (ENSG00000150907), FOXH1 (ENSG00000160973), FOXQ1 (ENSG00000164379), FOXK1 (ENSG00000164916), FOXD4 (ENSG00000170122), FOXA3 (ENSG00000170608), FOXB1 (ENSG00000171956), FOXR1 (ENSG00000176302), FOXL1 (ENSG00000176678), FOXC2 (ENSG00000176692), FOXE1 (ENSG00000178919), FOXS1 (ENSG00000179772), FOXL2 (ENSG00000183770), FOXO4 (ENSG00000184481), FOXD4L1 (ENSG00000184492), FOXD4L4 (ENSG00000184659), FOXD2 (ENSG00000186564), FOXI2 (ENSG00000186766), FOXE3 (ENSG00000186790), FOXD3 (ENSG00000187140), FOXD4L3 (ENSG00000187559), FOXR2 (ENSG00000189299), FOXJ3 (ENSG00000198815), FOXO6 (ENSG00000204060), FOXB2 (ENSG00000204612), FOXD4L5 (ENSG00000204779), FOXI3 (ENSG00000214336), FOXD1 (ENSG00000251493)

Protein

Protein identifiers

Forkhead box protein L3 — A0A1W2PRP0 (reviewed: A0A1W2PRP0)

All UniProt accessions (2): A0A1W2PRP0, A0A1W2PRW6

UniProt curated annotations — full annotation on UniProt →

Function. Probable transcriptional regulator.

Subcellular location. Nucleus.

RefSeq proteins (1): NP_001361767* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001766	Fork_head_dom	Domain
IPR030456	TF_fork_head_CS_2	Conserved_site
IPR036388	WH-like_DNA-bd_sf	Homologous_superfamily
IPR036390	WH_DNA-bd_sf	Homologous_superfamily
IPR050211	FOX_domain-containing	Family

Pfam: PF00250

UniProt features (6 total): compositionally biased region 3, chain 1, DNA-binding region 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1W2PRP0-F1	68.41	0.28

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 1 (showing top): chr7p22

GO Biological Process (4): regulation of transcription by RNA polymerase II (GO:0006357), anatomical structure morphogenesis (GO:0009653), cell differentiation (GO:0030154), regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (5): 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 (GO:0003677), DNA-binding transcription factor activity (GO:0003700), sequence-specific DNA binding (GO:0043565)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA-templated transcription	2
RNA polymerase II transcription regulatory region sequence-specific DNA binding	2
transcription by RNA polymerase II	1
developmental process	1
anatomical structure development	1
cellular developmental process	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	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
nucleic acid binding	1
transcription cis-regulatory region binding	1
transcription regulator activity	1
DNA binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

180 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FOXL3	DMRT1	Q9Y5R6	588
FOXL3	FBXO47	Q5MNV8	507
FOXL3	AMH	P03971	445
FOXL3	KLHL23	Q8NBE8	437
FOXL3	DMRT2	Q9Y5R5	432
FOXL3	CYP19A1	P11511	416
FOXL3	DMRTA2	Q96SC8	409
FOXL3	DMRT3	Q9NQL9	383
FOXL3	FIGLA	Q6QHK4	381
FOXL3	REC8	O95072	377
FOXL3	BMP15	O95972	371
FOXL3	AMHR2	Q16671	362
FOXL3	NANOS2	P60321	354
FOXL3	RSPO1	Q2MKA7	353
FOXL3	NR5A1	Q13285	333

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1W2PRP0, A6NCS4, A7Y7W2, O14512, O43638, O57601, O70220, O96004, P07812, P09023, P10085, P10284, P17483, P22091, P24899, P50548, P52954, P52955, P55318, P57100, P63156, P63157, P70447, P79772, P97832, Q02346, Q05917, Q0VCE2, Q12952, Q1XID0, Q28555, Q3I5G5, Q3Y598, Q60688, Q61660, Q63244, Q63250, Q64279, Q64305, Q64731

Diamond homologs: A0A078BQN7, A0A1W2PRP0, A0A8V0YY16, A1L1S5, A3KNJ3, A8MTJ6, A8XJN7, B5RHS5, D3Z120, F1R8Z9, O00358, O17617, O43638, O54743, O60129, O88470, P32027, P32028, P32030, P32315, P42128, P55316, P56260, P58012, P79772, P85037, P91278, Q00939, Q01167, Q02360, Q12946, Q12947, Q12948, Q12950, Q12951, Q12952, Q13461, Q19802, Q1A1A1, Q1A1A2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	4
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

1515 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:290741:T:C	F66L	1.000
7:290743:C:A	F66L	1.000
7:290743:C:G	F66L	1.000
7:290771:T:A	W76R	1.000
7:290771:T:C	W76R	1.000
7:290773:G:C	W76C	1.000
7:290773:G:T	W76C	1.000
7:290778:A:T	N78I	1.000
7:290779:C:A	N78K	1.000
7:290779:C:G	N78K	1.000
7:290781:C:T	S79F	1.000
7:290784:T:A	I80N	1.000
7:290784:T:G	I80S	1.000
7:290786:C:A	R81S	1.000
7:290789:C:A	H82N	1.000
7:290789:C:G	H82D	1.000
7:290790:A:T	H82L	1.000
7:290791:C:A	H82Q	1.000
7:290791:C:G	H82Q	1.000
7:290794:C:A	N83K	1.000
7:290794:C:G	N83K	1.000
7:290796:T:A	L84Q	1.000
7:290796:T:C	L84P	1.000
7:290813:T:C	F90L	1.000
7:290814:T:C	F90S	1.000
7:290814:T:G	F90C	1.000
7:290815:C:A	F90L	1.000
7:290815:C:G	F90L	1.000
7:291105:T:A	W107R	1.000
7:291105:T:C	W107R	1.000

dbSNP variants (sampled 300 via entrez): RS1000045791 (7:289554 C>A), RS1000676876 (7:289716 C>T), RS1000977396 (7:291235 C>G,T), RS1001000109 (7:288394 C>T), RS1001029776 (7:291037 C>A,T), RS1001550364 (7:289218 A>C,G), RS1001766385 (7:289503 G>A), RS1002772357 (7:288334 G>A), RS1003033346 (7:289069 G>A,T), RS1003394209 (7:291903 A>G), RS1004906027 (7:291566 C>G), RS1005105364 (7:289524 AC>A,ACC), RS1005125466 (7:291817 A>G), RS1005852015 (7:288315 A>C), RS1005930978 (7:291707 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.