FOXL2NB

Summary

FOXL2NB (FOXL2 neighbor, HGNC:34428) is a protein-coding gene on chromosome 3q22.3, encoding FOXL2 neighbor protein (Q6ZUU3).

Located in fibrillar center.

Source: NCBI Gene 401089 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 30 total — 1 pathogenic
• MANE Select transcript: NM_001040061

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34428
Approved symbol	FOXL2NB
Name	FOXL2 neighbor
Location	3q22.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ43329
Ensembl gene	ENSG00000206262
Ensembl biotype	protein_coding
Entrez	401089

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000383165, ENST00000470680, ENST00000498709, ENST00000959845

RefSeq mRNA: 1 — MANE Select: NM_001040061 NM_001040061

CCDS: CCDS43155

Canonical transcript exons

ENST00000383165 — 3 exons

Exon	Start	End
ENSE00001495181	138950265	138953990
ENSE00001507208	138949520	138949639
ENSE00003849199	138947217	138947464

Expression profiles

Bgee: expression breadth broad, 72 present calls, max score 93.75.

FANTOM5 (CAGE): breadth broad, TPM avg 1.2141 / max 68.2098, expressed in 312 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
38815	0.4346	213
38816	0.3962	201
38814	0.2940	99
38818	0.0401	21
38819	0.0382	16
38817	0.0111	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left ovary	UBERON:0002119	93.75	gold quality
stromal cell of endometrium	CL:0002255	93.58	gold quality
ovary	UBERON:0000992	92.30	gold quality
right ovary	UBERON:0002118	89.83	gold quality
endocervix	UBERON:0000458	87.13	gold quality
endometrium	UBERON:0001295	86.50	gold quality
left uterine tube	UBERON:0001303	84.38	gold quality
fallopian tube	UBERON:0003889	83.48	gold quality
uterine cervix	UBERON:0000002	80.02	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	79.58	gold quality
right uterine tube	UBERON:0001302	79.57	gold quality
pituitary gland	UBERON:0000007	79.13	gold quality
ectocervix	UBERON:0012249	77.98	gold quality
body of uterus	UBERON:0009853	76.10	gold quality
adenohypophysis	UBERON:0002196	74.84	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	74.62	gold quality
myometrium	UBERON:0001296	73.42	gold quality
vagina	UBERON:0000996	68.88	gold quality
right adrenal gland cortex	UBERON:0035827	67.96	gold quality
right adrenal gland	UBERON:0001233	66.36	gold quality
left adrenal gland	UBERON:0001234	65.11	gold quality
smooth muscle tissue	UBERON:0001135	64.29	gold quality
left adrenal gland cortex	UBERON:0035825	63.89	gold quality
adrenal gland	UBERON:0002369	62.38	gold quality
testis	UBERON:0000473	60.12	gold quality
left testis	UBERON:0004533	58.77	gold quality
right testis	UBERON:0004534	57.39	gold quality
placenta	UBERON:0001987	56.73	gold quality
lower esophagus mucosa	UBERON:0035834	55.67	gold quality
substantia nigra	UBERON:0002038	54.73	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.55

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

155 targeting FOXL2NB, 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-8485	100.00	77.57	4731
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-432-3P	100.00	67.86	705
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-7110-3P	100.00	73.18	2486
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-4481	100.00	66.42	1669
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-3910	99.95	71.13	2227

Literature-anchored findings (GeneRIF, showing 1)

• This study presents a new upstream regulator of FOXL2 and demonstrats that this new STAT3-FOXL2 pathway has an important function in HeLaHeLa cell apoptosis, providing new insights regarding the targeting of FOXL2 for cancer prevention and treatment. (PMID:31221094)

Cross-species orthologs

0 orthologs

Protein

Protein identifiers

FOXL2 neighbor protein — Q6ZUU3 (reviewed: Q6ZUU3)

All UniProt accessions (2): Q6ZUU3, F8WBY5

RefSeq proteins (1): NP_001035150* (*=MANE)

Domains & families (InterPro)

UniProt features (3 total): region of interest 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZUU3-F1	48.70	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 28 (showing top): chr3q22, GOCC_NUCLEOLUS, GOCC_FIBRILLAR_CENTER, LMTK3_TARGET_GENES, TAFAZZIN_TARGET_GENES, MIR8485, MIR616_5P, MIR371B_5P, MIR373_5P, MIR3910, MIR6878_5P, MIR519A_2_5P_MIR520B_5P, MIR6127, MIR217_5P, MIR6129

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): fibrillar center (GO:0001650)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
nucleolus	1
cellular anatomical structure	1

Protein interactions and networks

STRING

118 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FOXL2NB	RFPL1	O75677	582
FOXL2NB	GARIN5A	Q6IPT2	578
FOXL2NB	KCNJ18	B7U540	571
FOXL2NB	SPINK6	Q6UWN8	512
FOXL2NB	ZNF853	P0CG23	507
FOXL2NB	ZNF570	Q96NI8	507
FOXL2NB	LRRC23	Q53EV4	447
FOXL2NB	GPATCH4	Q5T3I0	416
FOXL2NB	PCOLCE2	Q9UKZ9	411
FOXL2NB	MAP7D2	Q96T17	376
FOXL2NB	KRI1	Q8N9T8	370
FOXL2NB	GNPDA1	P46926	307
FOXL2NB	METTL5	Q9NRN9	305
FOXL2NB	ULBP2	Q9BZM5	300
FOXL2NB	PRR19	A6NJB7	290

IntAct

0 interactions, top by confidence:

BioGRID (1): FOXL2NB (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GUT2, A0A3Q1LFG5, A1L4Q6, A2RUQ5, A8MQB3, A8MU10, A8MZ25, B1ANY3, C9JC47, P0C7V0, P0C864, P0CG42, P0CG43, P0DP75, P0DPA3, P0DXC1, P20975, P20977, P24026, P59020, P59021, P87743, Q06250, Q0IIN9, Q52M75, Q5SR53, Q5T036, Q5W150, Q67923, Q6ZUF6, Q6ZUU3, Q71F78, Q7Z4H9, Q8IYB0, Q8JMY5, Q8JMZ5, Q8JN06, Q8N2X6, Q8N5N4, Q8N9X3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	25
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
562821	GRCh37/hg19 3q22.3-23(chr3:138525030-139146538)x1	Pathogenic

SpliceAI

484 predictions. Top by Δscore:

Variant	Effect	Δscore
3:138947412:G:GT	donor_gain	1.0000
3:138947433:A:T	donor_gain	1.0000
3:138947460:TTCAG:T	donor_loss	0.9900
3:138947461:TCAGG:T	donor_loss	0.9900
3:138947462:CAG:C	donor_loss	0.9900
3:138947463:AG:A	donor_loss	0.9900
3:138947464:GGTGA:G	donor_loss	0.9900
3:138947465:G:GC	donor_loss	0.9900
3:138947466:T:G	donor_loss	0.9900
3:138947432:G:GT	donor_gain	0.9700
3:138947512:GC:G	donor_gain	0.9700
3:138948789:G:GT	donor_gain	0.9600
3:138948761:GCCTC:G	donor_gain	0.9400
3:138947468:A:T	donor_gain	0.9300
3:138948790:G:T	donor_gain	0.9300
3:138950335:G:T	donor_gain	0.9300
3:138948806:G:GA	donor_gain	0.9200
3:138950048:A:T	acceptor_gain	0.8500
3:138950047:CAG:C	acceptor_gain	0.8300
3:138949510:A:AG	acceptor_gain	0.8200
3:138949511:G:GG	acceptor_gain	0.8200
3:138950045:CCCAG:C	acceptor_gain	0.8200
3:138950046:CCA:C	acceptor_gain	0.8100
3:138947806:TTG:T	donor_gain	0.8000
3:138949299:GTAAC:G	acceptor_gain	0.8000
3:138950044:CCCCA:C	acceptor_gain	0.8000
3:138950049:G:T	acceptor_gain	0.8000
3:138948793:G:GT	donor_gain	0.7900
3:138949511:G:C	acceptor_gain	0.7900
3:138947340:C:CG	donor_gain	0.7800

AlphaMissense

1079 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:138950435:T:C	F131L	0.920
3:138950437:C:A	F131L	0.920
3:138950437:C:G	F131L	0.920
3:138950524:G:C	W160C	0.818
3:138950524:G:T	W160C	0.818
3:138950547:A:T	K168I	0.792
3:138950274:T:C	I77T	0.767
3:138950536:C:G	C164W	0.757
3:138950563:T:G	C173W	0.756
3:138950534:T:A	C164S	0.755
3:138950535:G:C	C164S	0.755
3:138950534:T:C	C164R	0.753
3:138950455:C:A	N137K	0.735
3:138950455:C:G	N137K	0.735
3:138950561:T:A	C173S	0.731
3:138950562:G:C	C173S	0.731
3:138950561:T:C	C173R	0.724
3:138950562:G:A	C173Y	0.698
3:138950522:T:A	W160R	0.695
3:138950522:T:C	W160R	0.695
3:138949596:G:A	M59I	0.694
3:138949596:G:C	M59I	0.694
3:138949596:G:T	M59I	0.694
3:138950436:T:G	F131C	0.691
3:138950436:T:C	F131S	0.666
3:138949593:G:C	K58N	0.661
3:138949593:G:T	K58N	0.661
3:138949599:C:G	C60W	0.661
3:138950549:G:T	G169W	0.648
3:138949597:T:C	C60R	0.630

dbSNP variants (sampled 300 via entrez): RS1000004840 (3:138952060 A>C,G), RS1000078768 (3:138945417 G>A), RS1000605636 (3:138950683 G>A), RS1000923858 (3:138950319 G>A,T), RS1001629364 (3:138948800 A>C,G), RS1002549130 (3:138954440 T>C,G), RS1002779155 (3:138953773 C>T), RS1002803674 (3:138953497 G>GTA), RS1003037092 (3:138947161 TC>T), RS1003189216 (3:138947612 A>G,T), RS1003632435 (3:138945701 G>A,T), RS1003818482 (3:138952169 G>A), RS1004149032 (3:138950754 C>G,T), RS1004645796 (3:138947713 T>C), RS1005683265 (3:138952476 T>A)

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

1 associations (top):

Study	Trait	p-value
GCST006661_139	Male-pattern baldness	3.000000e-19

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

11 total (human), top 11 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	increases expression	1
ethyl-p-hydroxybenzoate	increases expression	1
beta-lapachone	decreases expression	1
sodium arsenite	decreases expression	1
abrine	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Testosterone	decreases expression	1
Valproic Acid	increases methylation	1
Cyclosporine	decreases methylation	1

Clinical trials (associated diseases)

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