FNBP4

gene
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Also known as KIAA1014

Summary

FNBP4 (formin binding protein 4, HGNC:19752) is a protein-coding gene on chromosome 11p11.2, encoding Formin-binding protein 4 (Q8N3X1). It is a selective cancer dependency (DepMap: 60.3% of cell lines).

This gene encodes a protein containing two tryptophan-rich WW domains that binds the proline-rich formin homology 1 domains of formin family proteins, suggesting a role in the regulation of cytoskeletal dynamics during cell division and migration. It also binds intersectin family proteins suggesting a role in the maintenance of membrane curvature at sites of nascent vesicle formation. Naturally occurring mutations in this gene are associated with Waardenburg anophthalmia syndrome.

Source: NCBI Gene 23360 — RefSeq curated summary.

At a glance

  • GWAS associations: 15
  • Clinical variants (ClinVar): 153 total
  • Cancer dependency (DepMap): dependent in 60.3% of screened cell lines
  • MANE Select transcript: NM_015308

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:19752
Approved symbolFNBP4
Nameformin binding protein 4
Location11p11.2
Locus typegene with protein product
StatusApproved
AliasesKIAA1014
Ensembl geneENSG00000109920
Ensembl biotypeprotein_coding
OMIM615265
Entrez23360

Gene structure

Transcript identifiers

Ensembl transcripts: 19 — 11 protein_coding_CDS_not_defined, 5 protein_coding, 3 retained_intron

ENST00000263773, ENST00000524696, ENST00000525316, ENST00000525792, ENST00000526109, ENST00000527894, ENST00000528388, ENST00000529156, ENST00000530207, ENST00000531394, ENST00000532646, ENST00000533707, ENST00000534003, ENST00000540172, ENST00000542975, ENST00000544590, ENST00000883715, ENST00000917808, ENST00000961496

RefSeq mRNA: 2 — MANE Select: NM_015308 NM_001318339, NM_015308

CCDS: CCDS41644

Canonical transcript exons

ENST00000263773 — 17 exons

ExonStartEnd
ENSE000008393564772446847724778
ENSE000021826924771649447717512
ENSE000022663604776706947767341
ENSE000034679654772297647723316
ENSE000034811224771992947720086
ENSE000034925694775452847754664
ENSE000035356974773137447731561
ENSE000035382994772402847724172
ENSE000035554804774395347744163
ENSE000035610144776527047765362
ENSE000035668604773253747732670
ENSE000035703084775114347751290
ENSE000035725074775091647751036
ENSE000035913684775291647753102
ENSE000036226004774605647746394
ENSE000036539234773661647736740
ENSE000036653134773402547734129

Expression profiles

Bgee: expression breadth ubiquitous, 207 present calls, max score 98.37.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 56.9597 / max 898.3696, expressed in 1826 samples.

FANTOM5 promoters (7 alternative TSS)

Promoter IDTPM avgSamples expressed
11966948.98481826
1196684.35301624
1196731.0772463
1196700.9878484
1196710.7607376
1196720.5594266
1196740.236895

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
sural nerveUBERON:001548898.37gold quality
mucosa of stomachUBERON:000119998.34gold quality
calcaneal tendonUBERON:000370198.33gold quality
left ovaryUBERON:000211998.27gold quality
body of uterusUBERON:000985398.22gold quality
right ovaryUBERON:000211898.21gold quality
endocervixUBERON:000045898.18gold quality
body of pancreasUBERON:000115098.15gold quality
right uterine tubeUBERON:000130298.11gold quality
left lobe of thyroid glandUBERON:000112098.01gold quality
right lobe of thyroid glandUBERON:000111997.96gold quality
nerveUBERON:000102197.94gold quality
tibial nerveUBERON:000132397.94gold quality
skin of legUBERON:000151197.83gold quality
vermiform appendixUBERON:000115497.76gold quality
ectocervixUBERON:001224997.74gold quality
right hemisphere of cerebellumUBERON:001489097.68gold quality
cerebellar hemisphereUBERON:000224597.67gold quality
skin of abdomenUBERON:000141697.66gold quality
left uterine tubeUBERON:000130397.58gold quality
cerebellar cortexUBERON:000212997.54gold quality
adrenal tissueUBERON:001830397.54gold quality
ventricular zoneUBERON:000305397.50gold quality
small intestine Peyer’s patchUBERON:000345497.50gold quality
minor salivary glandUBERON:000183097.47gold quality
granulocyteCL:000009497.41gold quality
right lungUBERON:000216797.40gold quality
rectumUBERON:000105297.34gold quality
muscle layer of sigmoid colonUBERON:003580597.18gold quality
esophagogastric junction muscularis propriaUBERON:003584197.18gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.95

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TP53

miRNA regulators (miRDB)

121 targeting FNBP4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-4776-3P100.0068.731340
HSA-MIR-3163100.0077.238605
HSA-MIR-4262100.0073.263931
HSA-MIR-3689D100.0066.141181
HSA-MIR-6851-5P100.0065.631294
HSA-MIR-340-5P100.0072.504437
HSA-MIR-453199.9969.703181
HSA-MIR-548AW99.9972.573559
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-499A-5P99.9870.791323
HSA-MIR-25-3P99.9874.601817
HSA-MIR-32-5P99.9875.211964
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-MIR-3617-3P99.9867.86918
HSA-MIR-548AN99.9770.912817
HSA-MIR-146A-5P99.9668.93988
HSA-MIR-146B-5P99.9669.13977
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-7153-5P99.9468.891006
HSA-MIR-539-5P99.9370.302855

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 60.3% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 1)

  • A c.683C>T (p.Thr228Met) mutation in FNBP4 was found as a primary candidate to microphthalmia with limb anomalies (PMID:23703728)

Cross-species orthologs

8 orthologs

OrganismSymbolGene ID
danio_reriofnbp4ENSDARG00000051800
mus_musculusFnbp4ENSMUSG00000008200
rattus_norvegicusFnbp4ENSRNOG00000007241
drosophila_melanogasterFrlFBGN0267795
caenorhabditis_elegansWBGENE00018976
caenorhabditis_elegansWBGENE00019030
caenorhabditis_eleganssydn-1WBGENE00021473
caenorhabditis_elegansWBGENE00021698

Paralogs (18): DAAM1 (ENSG00000100592), DIAPH1 (ENSG00000131504), FHOD3 (ENSG00000134775), FHOD1 (ENSG00000135723), FHDC1 (ENSG00000137460), DIAPH3 (ENSG00000139734), DAAM2 (ENSG00000146122), DIAPH2 (ENSG00000147202), FMN2 (ENSG00000155816), FMNL2 (ENSG00000157827), FMNL3 (ENSG00000161791), FMNL1 (ENSG00000184922), FAM47A (ENSG00000185448), SHTN1 (ENSG00000187164), FAM47B (ENSG00000189132), FAM47C (ENSG00000198173), INF2 (ENSG00000203485), GRID2IP (ENSG00000215045)

Protein

Protein identifiers

Formin-binding protein 4Q8N3X1 (reviewed: Q8N3X1)

Alternative names: Formin-binding protein 30

All UniProt accessions (2): Q8N3X1, F5GXL1

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Binds FMN1. Interacts with the Arg/Gly-rich-flanked Pro-rich of KHDRBS1/SAM68. Arginine methylation in these regions has no effect on this binding.

Tissue specificity. Highly expressed in the eye.

Domain organisation. These WW domains interact with Arg/Gly-rich-flanked Pro-rich domains found in several WW domain-binding proteins (WBPs). The N-terminal WW domain has the greater ligand-binding ability.

Isoforms (2)

UniProt IDNamesCanonical?
Q8N3X1-11yes
Q8N3X1-22

RefSeq proteins (2): NP_001305268, NP_056123* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001202WW_domDomain
IPR036020WW_dom_sfHomologous_superfamily
IPR053076WW_domain_proteinFamily

Pfam: PF00397

UniProt features (56 total): modified residue 19, compositionally biased region 17, region of interest 6, cross-link 6, sequence variant 3, domain 2, chain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N3X1-F156.840.15

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 (25): 18, 116, 124, 172, 290, 427, 432, 435, 438, 442, 464, 479, 499, 508, 516, 517, 963, 964, 965, 301 …

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 209 (showing top): MODULE_255, BROWNE_HCMV_INFECTION_8HR_UP, MODULE_317, ONKEN_UVEAL_MELANOMA_UP, FOSTER_TOLERANT_MACROPHAGE_UP, FISCHER_G2_M_CELL_CYCLE, OCT1_03, FISCHER_DREAM_TARGETS, BILBAN_B_CLL_LPL_DN, DELASERNA_MYOD_TARGETS_DN, MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_UP, CHANDRAN_METASTASIS_UP, GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN, MODULE_69, CHEN_HOXA5_TARGETS_9HR_UP

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): nucleoplasm (GO:0005654)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding1
nuclear lumen1
cellular anatomical structure1

Protein interactions and networks

STRING

1719 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
FNBP4WBP4O75554687
FNBP4GRID2IPA4D2P6630
FNBP4FMNL3Q8IVF7604
FNBP4FMN1Q68DA7595
FNBP4DAAM2Q86T65594
FNBP4FMNL1O95466590
FNBP4DIAPH2O60879579
FNBP4FMNL2Q96PY5575
FNBP4LENG8Q96PV6551
FNBP4NUP160Q12769543
FNBP4DAAM1Q9Y4D1543
FNBP4DIAPH1O60610534
FNBP4PFN4Q8NHR9529
FNBP4PFN3P60673526
FNBP4FHOD1Q9Y613524

IntAct

55 interactions, top by confidence:

ABTypeScore
FNBP4PRPF40Apsi-mi:“MI:0914”(association)0.550
FNBP4PRPF40Apsi-mi:“MI:0915”(physical association)0.550
KHDRBS1FNBP4psi-mi:“MI:0407”(direct interaction)0.540
KHDRBS1FNBP4psi-mi:“MI:0915”(physical association)0.540
BAG2HGSpsi-mi:“MI:0914”(association)0.530
ZC3H18AQRpsi-mi:“MI:0914”(association)0.530
ZC3H18SRPK2psi-mi:“MI:0914”(association)0.530
FNBP4H2BC21psi-mi:“MI:0915”(physical association)0.400
HSCBFNBP4psi-mi:“MI:0915”(physical association)0.370
PLXNA2FNBP4psi-mi:“MI:0915”(physical association)0.370
HTTFNBP4psi-mi:“MI:0915”(physical association)0.370
FNBP4HTTpsi-mi:“MI:0915”(physical association)0.370
Psmb4PSMD14psi-mi:“MI:0914”(association)0.350
JUNpsi-mi:“MI:0914”(association)0.350
CEP135MCRIP1psi-mi:“MI:0914”(association)0.350
CEP135WWP2psi-mi:“MI:0914”(association)0.350
CEP135WDR91psi-mi:“MI:0914”(association)0.350
RBM39RPS3Apsi-mi:“MI:0914”(association)0.350
hspa1a_hspa1b_human-1SHTN1psi-mi:“MI:0914”(association)0.350
BAG1PSMD11psi-mi:“MI:0914”(association)0.350
FGF12SUPT5Hpsi-mi:“MI:0914”(association)0.350
ARHGAP12WASLpsi-mi:“MI:0914”(association)0.350
TGM1DNM1Lpsi-mi:“MI:0914”(association)0.350
HSPA2HGSpsi-mi:“MI:0914”(association)0.350

BioGRID (99): FNBP4 (Affinity Capture-RNA), FNBP4 (Affinity Capture-RNA), FNBP4 (Proximity Label-MS), FNBP4 (Affinity Capture-MS), FNBP4 (Affinity Capture-MS), FNBP4 (Affinity Capture-MS), FNBP4 (Affinity Capture-RNA), FNBP4 (Affinity Capture-RNA), FNBP4 (Affinity Capture-MS), FNBP4 (Affinity Capture-MS), FNBP4 (Affinity Capture-MS), FNBP4 (Proximity Label-MS), FNBP4 (Affinity Capture-MS), FNBP4 (Proximity Label-MS), FNBP4 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTU1, A2AUY4, B7ZS37, D3Z8Y2, D4A4L4, D4A666, E1B7L7, O46385, O60293, O75152, O95425, P0DQW0, Q08AZ1, Q3KQW7, Q3U1C4, Q3UH68, Q3ZC82, Q4G0F8, Q4V9H5, Q5F3Z9, Q5NBX1, Q5REG6, Q5ZJJ1, Q5ZM88, Q61464, Q62394, Q68FE9, Q6NZF1, Q6PJT7, Q6ZQ03, Q6ZU65, Q76L83, Q7TMD5, Q8BHZ4, Q8BJ05, Q8BLG0, Q8BZ32, Q8C9B9, Q8CCJ9, Q8K298

Diamond homologs: Q6ZQ03, Q8N3X1

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 68 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
mRNA Polyadenylation914.9×1e-06
mRNA Splicing612.4×6e-04
Processing of Capped Intron-Containing Pre-mRNA812.4×2e-05
mRNA Splicing - Major Pathway1212.4×5e-08
Dengue Virus-Host Interactions108.6×2e-05
Metabolism of RNA86.3×2e-03

GO biological processes:

GO termPartnersFoldFDR
mRNA splicing, via spliceosome812.2×6e-05
mRNA processing911.8×3e-05
RNA splicing710.3×8e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance101
Likely benign9
Benign11

Top pathogenic / likely-pathogenic (0)

SpliceAI

3023 predictions. Top by Δscore:

VariantEffectΔscore
11:47717508:TGCCA:Tacceptor_gain1.0000
11:47717510:CCA:Cacceptor_gain1.0000
11:47717511:CA:Cacceptor_gain1.0000
11:47717511:CAC:Cacceptor_gain1.0000
11:47717513:C:CCacceptor_gain1.0000
11:47719932:A:Cdonor_gain1.0000
11:47719933:CCAG:Cdonor_gain1.0000
11:47720084:TGC:Tacceptor_gain1.0000
11:47720087:C:CCacceptor_gain1.0000
11:47722988:T:TAdonor_gain1.0000
11:47724171:CT:Cacceptor_gain1.0000
11:47731368:TCTCA:Tdonor_loss1.0000
11:47731369:CTCAC:Cdonor_loss1.0000
11:47731370:TCA:Tdonor_loss1.0000
11:47731371:CA:Cdonor_loss1.0000
11:47731372:A:ACdonor_gain1.0000
11:47731373:C:CCdonor_gain1.0000
11:47731373:C:Tdonor_loss1.0000
11:47731557:GATCC:Gacceptor_gain1.0000
11:47731558:ATCC:Aacceptor_gain1.0000
11:47731559:TCC:Tacceptor_gain1.0000
11:47731560:CC:Cacceptor_gain1.0000
11:47731560:CCC:Cacceptor_gain1.0000
11:47731561:CC:Cacceptor_gain1.0000
11:47731561:CCT:Cacceptor_loss1.0000
11:47731562:C:CCacceptor_gain1.0000
11:47731562:C:Tacceptor_gain1.0000
11:47731567:T:Cacceptor_gain1.0000
11:47731567:T:TCacceptor_gain1.0000
11:47731901:ATTTC:Adonor_gain1.0000

AlphaMissense

6595 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:47717464:C:AW1004C1.000
11:47717464:C:GW1004C1.000
11:47717466:A:GW1004R1.000
11:47717466:A:TW1004R1.000
11:47720042:C:AW950C1.000
11:47720042:C:GW950C1.000
11:47720044:A:GW950R1.000
11:47720044:A:TW950R1.000
11:47731510:C:AW624C1.000
11:47731510:C:GW624C1.000
11:47731512:A:GW624R1.000
11:47731512:A:TW624R1.000
11:47731542:A:CY614D1.000
11:47731550:C:GR611P1.000
11:47732542:C:AW605C1.000
11:47732542:C:GW605C1.000
11:47732543:C:GW605S1.000
11:47732544:A:GW605R1.000
11:47732544:A:TW605R1.000
11:47732550:A:GC603R1.000
11:47732554:C:AW601C1.000
11:47732554:C:GW601C1.000
11:47732556:A:GW601R1.000
11:47732556:A:TW601R1.000
11:47732591:A:GL589P1.000
11:47732612:A:GL582P1.000
11:47732624:A:GL578P1.000
11:47732651:C:GR569P1.000
11:47732655:A:GW568R1.000
11:47732655:A:TW568R1.000

dbSNP variants (sampled 300 via entrez): RS1000167069 (11:47751287 C>A), RS1000200109 (11:47751023 C>A,G,T), RS1000295641 (11:47721483 G>A), RS1000304289 (11:47721463 T>C), RS1000381097 (11:47751442 G>A,C), RS1000430264 (11:47757293 C>T), RS1000452047 (11:47762224 C>T), RS1000511169 (11:47767473 T>C,G), RS1000533234 (11:47735239 T>C), RS1000565854 (11:47728315 T>C), RS1000615497 (11:47739832 G>A), RS1000646850 (11:47739630 A>G), RS1000671141 (11:47720708 A>T), RS1000735414 (11:47763546 G>A,C), RS1000793883 (11:47756629 T>A,C)

Disease associations

OMIM: gene MIM:615265 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

15 associations (top):

StudyTraitp-value
GCST004904_244Body mass index1.000000e-09
GCST005232_56Neuroticism1.000000e-16
GCST005905_14Global electrical heterogeneity phenotypes6.000000e-09
GCST006718_7Alcohol use disorder (consumption score)3.000000e-09
GCST006896_9Free thyroxine concentration8.000000e-11
GCST006923_11Loneliness1.000000e-07
GCST006924_13Loneliness (MTAG)1.000000e-08
GCST007559_27Sleep duration (short sleep)4.000000e-08
GCST007825_4Alzheimer’s disease or fasting glucose levels (pleiotropy)3.000000e-16
GCST007944_2Medication use (antiglaucoma preparations and miotics)1.000000e-08
GCST010002_238Refractive error2.000000e-14
GCST010136_2Fruit consumption5.000000e-09
GCST010703_36Brain morphology (MOSTest)8.000000e-09
GCST011369_19Iron status biomarkers (ferritin levels)3.000000e-13
GCST90000025_155Appendicular lean mass3.000000e-37

EFO canonical traits (9, from GWAS)

EFO IDTrait name
EFO:0004340body mass index
EFO:0007660neuroticism measurement
EFO:0004327electrocardiography
EFO:0007865loneliness measurement
EFO:0009944Antiglaucoma preparations and miotics use measurement
EFO:0008111diet measurement
EFO:0004346neuroimaging measurement
EFO:0004459ferritin measurement
EFO:0004980appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects expression, decreases expression4
bisphenol Adecreases expression, decreases methylation, affects cotreatment3
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression2
aristolochic acid Idecreases expression1
GSK-J4increases expression1
FR900359increases phosphorylation1
TAK-243decreases sumoylation1
methylmercuric chlorideincreases expression1
triphenyl phosphateaffects expression1
tris(2-butoxyethyl) phosphateaffects expression1
cobaltous chlorideincreases expression1
manganese chlorideincreases abundance, increases expression1
coumarindecreases phosphorylation1
beta-methylcholineaffects expression1
K 7174increases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
abrineincreases expression1
Temozolomideincreases expression1
Arsenic Trioxideincreases expression1
Vorinostatdecreases expression1
Leflunomideincreases expression1
Air Pollutants, Occupationalaffects expression, increases abundance, increases expression1
Vehicle Emissionsincreases abundance, increases expression1
Benzo(a)pyreneincreases methylation1
Cadmiumdecreases expression, increases abundance1
Caffeineaffects phosphorylation1
Cisplatindecreases expression1
Demecolcineincreases expression1
Dexamethasoneaffects cotreatment, decreases expression1
Dimethyl Sulfoxideincreases expression1

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.