FSCN3

gene

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Summary

FSCN3 (fascin actin-bundling protein 3, HGNC:3961) is a protein-coding gene on chromosome 7q32.1, encoding Fascin-3 (Q9NQT6). Acts as an actin bundling protein.

Predicted to enable actin filament binding activity. Predicted to be involved in actin filament bundle assembly; cell migration; and establishment or maintenance of cell polarity. Predicted to be located in cytoskeleton. Predicted to be active in several cellular components, including lamellipodium; microvillus; and ruffle.

Source: NCBI Gene 29999 — RefSeq curated summary.

At a glance

GWAS associations: 2
Clinical variants (ClinVar): 89 total
Phenotypes (HPO): 1
MANE Select transcript: NM_020369

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:3961
Approved symbol	FSCN3
Name	fascin actin-bundling protein 3
Location	7q32.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000106328
Ensembl biotype	protein_coding
OMIM	615800
Entrez	29999

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 2 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000265825, ENST00000421705, ENST00000469242, ENST00000478328, ENST00000478821

RefSeq mRNA: 1 — MANE Select: NM_020369 NM_020369

CCDS: CCDS34746

Canonical transcript exons

ENST00000265825 — 7 exons

Exon	Start	End
ENSE00000720436	127596328	127596446
ENSE00000720445	127598435	127598594
ENSE00000720462	127599381	127599551
ENSE00000882268	127601623	127602144
ENSE00000882269	127600194	127600399
ENSE00000882270	127593736	127593997
ENSE00003577017	127595307	127596003

Expression profiles

Bgee: expression breadth ubiquitous, 162 present calls, max score 97.19.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.5208 / max 153.8200, expressed in 155 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
204683	0.3399	153
80892	0.1520	4
80891	0.0289	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	97.19	gold quality
male germ cell	CL:0000015	96.03	gold quality
left testis	UBERON:0004533	95.70	gold quality
right testis	UBERON:0004534	95.52	gold quality
testis	UBERON:0000473	92.55	gold quality
adult organism	UBERON:0007023	86.41	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.11	gold quality
granulocyte	CL:0000094	73.43	gold quality
tibialis anterior	UBERON:0001385	69.80	silver quality
type B pancreatic cell	CL:0000169	68.20	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	68.12	silver quality
olfactory bulb	UBERON:0002264	67.00	gold quality
epithelial cell of pancreas	CL:0000083	66.98	gold quality
diaphragm	UBERON:0001103	65.92	gold quality
cortical plate	UBERON:0005343	64.25	gold quality
ileal mucosa	UBERON:0000331	63.37	silver quality
tongue squamous epithelium	UBERON:0006919	61.79	gold quality
hindlimb stylopod muscle	UBERON:0004252	61.69	gold quality
cerebellar cortex	UBERON:0002129	60.57	gold quality
leukocyte	CL:0000738	60.56	gold quality
cerebellar hemisphere	UBERON:0002245	60.36	gold quality
prefrontal cortex	UBERON:0000451	59.87	gold quality
monocyte	CL:0000576	59.82	gold quality
mononuclear cell	CL:0000842	59.72	gold quality
right hemisphere of cerebellum	UBERON:0014890	59.63	gold quality
cerebellum	UBERON:0002037	59.31	gold quality
stromal cell of endometrium	CL:0002255	58.44	gold quality
pancreatic ductal cell	CL:0002079	58.41	silver quality
deltoid	UBERON:0001476	57.39	gold quality
quadriceps femoris	UBERON:0001377	57.34	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	30.88
E-ANND-3	yes	4.13

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting FSCN3, 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-7152-3P	99.97	67.47	849
HSA-MIR-6783-3P	99.89	67.92	2059
HSA-MIR-1343-3P	99.89	66.78	1815
HSA-MIR-6124	99.87	69.78	3551
HSA-MIR-6842-5P	99.80	67.54	1587
HSA-MIR-7110-5P	99.80	67.84	1712
HSA-MIR-2052	99.79	69.37	2031
HSA-MIR-3934-5P	99.67	64.04	846
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-1290	99.59	69.90	2079
HSA-MIR-6752-5P	99.59	67.32	1243
HSA-MIR-5004-3P	99.54	68.27	1371
HSA-MIR-3171	99.49	69.06	776
HSA-MIR-122B-5P	99.46	70.81	1457
HSA-MIR-19A-5P	99.36	66.93	1675
HSA-MIR-19B-1-5P	99.36	67.07	1669
HSA-MIR-19B-2-5P	99.36	67.07	1669
HSA-MIR-1244	99.33	68.38	832
HSA-MIR-8065	99.19	70.38	1289
HSA-MIR-4254	99.11	65.15	1315
HSA-MIR-194-5P	99.01	69.65	1465
HSA-MIR-3074-5P	98.82	66.56	1414
HSA-MIR-6894-5P	98.70	63.78	809
HSA-MIR-3132	97.96	67.91	711
HSA-MIR-197-5P	97.23	68.10	596
HSA-MIR-4280	96.44	67.69	473
HSA-MIR-6735-3P	96.10	63.81	600
HSA-MIR-4522	95.76	66.23	742

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Fscn3	ENSMUSG00000029707
rattus_norvegicus	Fscn3	ENSRNOG00000007942
drosophila_melanogaster	sn	FBGN0003447

Paralogs (2): FSCN1 (ENSG00000075618), FSCN2 (ENSG00000186765)

Protein

Protein identifiers

Fascin-3 — Q9NQT6 (reviewed: Q9NQT6)

Alternative names: Testis fascin

All UniProt accessions (4): Q9NQT6, A0A140VK18, F8WDZ8, R4GN86

UniProt curated annotations — full annotation on UniProt →

Function. Acts as an actin bundling protein.

Subcellular location. Cytoplasm. Cytoskeleton.

Tissue specificity. Expressed in testis.

Similarity. Belongs to the fascin family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9NQT6-1	1	yes
Q9NQT6-2	2

RefSeq proteins (1): NP_065102* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008999	Actin-crosslinking	Homologous_superfamily
IPR010431	Fascin	Family
IPR022768	Fascin-like_dom	Domain
IPR024703	Fascin_metazoans	Family

Pfam: PF06268

UniProt features (6 total): splice variant 3, sequence variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NQT6-F1	92.19	0.83

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 73 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, GOBP_ACTIN_FILAMENT_BUNDLE_ORGANIZATION, GOBP_ESTABLISHMENT_OR_MAINTENANCE_OF_CELL_POLARITY, GOCC_RUFFLE, GOBP_ACTIN_FILAMENT_ORGANIZATION, chr7q32, GNF2_CCNA1, WEBER_METHYLATED_LCP_IN_SPERM_UP, VDR_Q3, GOMF_ACTIN_BINDING, GOCC_NEURON_PROJECTION, SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON_BY_RHO_GTPASES, GOCC_FILOPODIUM, GOCC_CELL_PROJECTION_MEMBRANE, GOCC_MICROVILLUS

GO Biological Process (4): establishment or maintenance of cell polarity (GO:0007163), cell migration (GO:0016477), actin filament bundle assembly (GO:0051017), actin filament organization (GO:0007015)

GO Molecular Function (3): protein-macromolecule adaptor activity (GO:0030674), actin filament binding (GO:0051015), actin binding (GO:0003779)

GO Cellular Component (9): ruffle (GO:0001726), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), microvillus (GO:0005902), actin cytoskeleton (GO:0015629), lamellipodium (GO:0030027), filopodium (GO:0030175), growth cone (GO:0030426), cell projection membrane (GO:0031253)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
plasma membrane bounded cell projection	3
cell leading edge	2
actin-based cell projection	2
cellular process	1
cell motility	1
cellular component assembly	1
actin filament bundle organization	1
actin cytoskeleton organization	1
supramolecular fiber organization	1
protein binding	1
molecular adaptor activity	1
actin binding	1
protein-containing complex binding	1
cytoskeletal protein binding	1
intracellular anatomical structure	1
cellular anatomical structure	1
intracellular membraneless organelle	1
actin filament bundle	1
cytoskeleton	1
site of polarized growth	1
distal axon	1
plasma membrane region	1

Protein interactions and networks

STRING

432 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
FSCN3	TMEM225	Q6GV28	673
FSCN3	FNDC8	Q8TC99	541
FSCN3	GCC1	Q96CN9	533
FSCN3	TMEM270	Q6UE05	532
FSCN3	IQCF1	Q8N6M8	525
FSCN3	GARIN1B	Q96KD3	524
FSCN3	GTSF1L	Q9H1H1	472
FSCN3	TMEM225B	P0DP42	460
FSCN3	CCDC182	A6NF36	443
FSCN3	KLHL10	Q6JEL2	442
FSCN3	SPATA3	Q8NHX4	436
FSCN3	ENTHD1	Q8IYW4	427
FSCN3	CCDC83	Q8IWF9	426
FSCN3	SPATS1	Q496A3	418
FSCN3	SPESP1	Q6UW49	407

IntAct

3 interactions, top by confidence:

A	B	Type	Score
FSCN3	PRAME	psi-mi:“MI:0914”(association)	0.530
FSCN3	PPP5C	psi-mi:“MI:0914”(association)	0.350

BioGRID (8): FLAD1 (Affinity Capture-MS), PRAME (Affinity Capture-MS), GLMN (Affinity Capture-MS), PRAME (Affinity Capture-MS), FLAD1 (Affinity Capture-MS), GLMN (Affinity Capture-MS), PPP5C (Affinity Capture-MS), FSCN3 (Affinity Capture-MS)

ESM2 similar proteins: B0LPN4, E9PZQ0, E9Q401, F1LMY4, O14926, O18728, O95834, P10767, P11403, P11716, P16960, P21658, P21817, P30957, P47823, P55075, P85845, Q13144, Q16658, Q24498, Q24524, Q32M02, Q3U7R1, Q4R4H3, Q5CZL1, Q5E9M9, Q5XGM5, Q61553, Q64350, Q6P6T4, Q6P9Z4, Q6PFQ7, Q6SZW1, Q7TNG5, Q7TSA0, Q7Z6L1, Q8CHW4, Q8IXI1, Q8JZN7, Q8K2J0

Diamond homologs: Q9NQT6, Q9QXW4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	76
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1303 predictions. Top by Δscore:

Variant	Effect	Δscore
7:127595295:T:TA	acceptor_gain	1.0000
7:127596442:CCCAG:C	donor_loss	1.0000
7:127596443:CCAG:C	donor_loss	1.0000
7:127596445:AGGTG:A	donor_loss	1.0000
7:127596446:GG:G	donor_loss	1.0000
7:127596448:T:A	donor_loss	1.0000
7:127598420:T:TA	acceptor_gain	1.0000
7:127598424:A:AG	acceptor_gain	1.0000
7:127598425:T:G	acceptor_gain	1.0000
7:127598430:TCCA:T	acceptor_loss	1.0000
7:127598431:CCA:C	acceptor_loss	1.0000
7:127598432:CA:C	acceptor_loss	1.0000
7:127598433:A:AC	acceptor_loss	1.0000
7:127598433:A:AG	acceptor_gain	1.0000
7:127598434:G:GT	acceptor_gain	1.0000
7:127598434:GA:G	acceptor_gain	1.0000
7:127598434:GAGGC:G	acceptor_gain	1.0000
7:127598592:CAGG:C	donor_loss	1.0000
7:127598594:GGT:G	donor_loss	1.0000
7:127598595:G:GG	donor_gain	1.0000
7:127599379:A:AG	acceptor_gain	1.0000
7:127599380:G:GG	acceptor_gain	1.0000
7:127599434:C:CA	acceptor_gain	1.0000
7:127599550:GG:G	donor_gain	1.0000
7:127599551:GG:G	donor_gain	1.0000
7:127601617:CTCCA:C	acceptor_loss	1.0000
7:127601618:TCCA:T	acceptor_loss	1.0000
7:127601619:CCAGG:C	acceptor_loss	1.0000
7:127601620:CA:C	acceptor_loss	1.0000
7:127601621:A:AC	acceptor_loss	1.0000

AlphaMissense

3263 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:127595568:T:A	W136R	0.997
7:127595568:T:C	W136R	0.997
7:127595475:T:A	W105R	0.995
7:127595475:T:C	W105R	0.995
7:127600211:T:A	W437R	0.995
7:127600211:T:C	W437R	0.995
7:127600388:T:A	W496R	0.993
7:127600388:T:C	W496R	0.993
7:127595570:G:C	W136C	0.990
7:127595570:G:T	W136C	0.990
7:127599546:T:C	F429S	0.989
7:127600394:T:C	F498L	0.989
7:127600396:T:A	F498L	0.989
7:127600396:T:G	F498L	0.989
7:127595446:T:C	F95S	0.986
7:127595569:G:C	W136S	0.985
7:127600265:T:C	F455L	0.985
7:127600267:C:A	F455L	0.985
7:127600267:C:G	F455L	0.985
7:127595701:T:C	F180S	0.984
7:127599432:T:C	L391S	0.983
7:127595632:C:A	A157D	0.982
7:127593917:A:C	S22R	0.979
7:127593919:C:A	S22R	0.979
7:127593919:C:G	S22R	0.979
7:127595509:T:C	L116S	0.979
7:127600266:T:C	F455S	0.979
7:127595310:T:A	W50R	0.978
7:127595310:T:C	W50R	0.978
7:127600208:T:C	F436L	0.978

dbSNP variants (sampled 300 via entrez): RS1000348397 (7:127602635 T>C), RS1000390954 (7:127596090 G>C), RS1000470891 (7:127602421 C>G), RS1000997314 (7:127592035 T>C), RS1001174520 (7:127591967 C>T), RS1002398372 (7:127598977 G>A), RS1002607068 (7:127594369 T>C), RS1002638187 (7:127594094 G>C), RS1002888335 (7:127598687 CG>C), RS1003359604 (7:127600231 C>T), RS1003821282 (7:127600523 C>T), RS1004279775 (7:127592559 G>A), RS1004316169 (7:127598938 C>A,T), RS1004364916 (7:127601909 C>T), RS1004419852 (7:127602307 A>C,G)

Disease associations

OMIM: gene MIM:615800 | disease phenotypes: MIM:300633

GenCC curated gene-disease

Mondo (1): hypospadias (MONDO:0005345)

Orphanet (1): OBSOLETE: Familial hypospadias (Orphanet:440)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPO	Term
HP:0000047	Hypospadias

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST003400_39	Type 2 diabetes	8.000000e-10
GCST012166_5	Adiponectin levels	7.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004502	adiponectin measurement

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D007021	Hypospadias	C12.050.351.875.466; C12.100.500.494.400; C12.200.294.494.400; C12.200.706.516; C12.800.516; C16.131.939.516

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases expression	2
aristolochic acid I	increases expression	1
triphenyl phosphate	affects expression	1
sodium arsenite	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
CGP 52608	affects binding, increases reaction	1
theaflavin-3,3’-digallate	affects expression	1
Endosulfan	decreases expression	1
Smoke	decreases expression	1
Acrylamide	increases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT02848157	PHASE4	COMPLETED	Effects of Dexmedetomidine as Adjunct to Pudendal Block for Pediatric Penile Surgery
NCT02861950	PHASE4	COMPLETED	Does Caudal Block Increase the Incidence of Urethrocutaneous Fistula Formation Following Hypospadias Repair in Infants?
NCT03902249	PHASE4	COMPLETED	Effect of Intravenous Dexamethasone With Pudendal Nerve Block on Postoperative Pain in Pediatric Hypospadias Repair
NCT05708989	PHASE4	WITHDRAWN	Caudal vs. Pudendal Block in Peds GU
NCT05837000	PHASE4	UNKNOWN	Dexmedetomidine, Ketamine and Magnesium Sulphate in Caudal Block for Hypospadias Repair
NCT05922605	PHASE4	UNKNOWN	Analgesic Effects of Caudal S-ketamine for Supplementation of Ropivacaine Caudal Analgesia in Children With Hypospadias
NCT07121764	PHASE4	COMPLETED	Postoperative Pain Relief in Children: Comparing Caudal Bupivacaine Alone Versus Bupivacaine With Dexmedetomidine for Infra-Umbilical Surgeries Under General Anesthesia
NCT07240649	PHASE4	NOT_YET_RECRUITING	Outcomes From Hyperbaric Oxygen (HBO2) Treatment for Emerging Indications
NCT01370798	PHASE3	COMPLETED	Local Oestrogen Versus Placebo as Preoperative Treatment in Patients With Severe Hypospadias: Effects on Post-operative Complications
NCT04423107	PHASE3	UNKNOWN	Assessment of Postop Hypospadias Pain
NCT04826484	PHASE3	TERMINATED	Opioid Reduction Initiative During Outpatient Pediatric Urologic Procedures Using Exparel
NCT07197203	PHASE3	NOT_YET_RECRUITING	Comparison of Caudal Block and Sacral Erector Spinae Plane Block With Dexmedetomidine in Pediatric Penile Hypospadias Repair
NCT05253456	PHASE2	COMPLETED	Modified Second Layer Repair for Distal Penile Hypospadias
NCT04479371	PHASE1	WITHDRAWN	Liposomal Bupivacaine vs Standard Penile Block for Hypospadias Repair
NCT02752308	PHASE2/PHASE3	COMPLETED	Effectiveness of Caudal Epidural Block on Intraoperative Blood Loss During Hypospadias Repair
NCT04876976	PHASE2/PHASE3	COMPLETED	Isoamyl 2-Cyanoacrylate in the Urethro-cutaneous Fistula Repair
NCT05093166	PHASE1/PHASE2	TERMINATED	Clinical Trial to Assess the Safety and Efficacy of Investigational Product in Patients Due to Hypospadias Treatment Failure
NCT04196400	EARLY_PHASE1	UNKNOWN	The Role of Local Long Acting Corticosteroid Injection in Hypospadias Surgery.
NCT01762007	Not specified	WITHDRAWN	The Change of the Detrusor Thickness After Hypospadias Repair - Comparison With the Normal Control Group
NCT01875640	Not specified	COMPLETED	Decision Support for Parents Receiving Information About Child’s Rare Disease
NCT02040389	Not specified	COMPLETED	Visual Guidelines and Tutoring in Pediatric Urological Surgery
NCT02096159	Not specified	ACTIVE_NOT_RECRUITING	Prophylactic Antibiotics or Placebo After Hypospadias Repair
NCT02103712	Not specified	COMPLETED	Long Term Outcome of Hypospadias Repair
NCT02162810	Not specified	TERMINATED	Effect of Steroids on Post-Operative Complications Following Proximal Hypospadias Repair
NCT02164682	Not specified	COMPLETED	The Effect of Caudal Block on the Postoperative Complications in Pediatric Patients After Hypospadias Repair
NCT02495090	Not specified	COMPLETED	Hypospadias and Exome: Identification of New Genes for Familial Hypospadias
NCT02497963	Not specified	UNKNOWN	Foreskin Graft Tubularized Incised Plate Urethroplasty vs Tubularized Incised Plate for Primary Hypospadias (FGTIP-TIP)
NCT02512887	Not specified	UNKNOWN	Caudal vs Local Anesthesia in Hypospadias
NCT02593903	Not specified	COMPLETED	Antibiotic Use Following Distal and Mid-shaft Hypospadias Repair
NCT02805491	Not specified	COMPLETED	Influence of Pesticide Exposure on the Occurrence of Hypospadias in Newborns in Picardie
NCT02851290	Not specified	COMPLETED	Effect of Caudal and Penile Block on Hypospadias Repair Complications
NCT03102554	Not specified	ENROLLING_BY_INVITATION	Genetics of Differences of Sex Development and Hypospadias
NCT03275519	Not specified	COMPLETED	Antibiotic Use in Distal Hypospadias Repair
NCT03575377	Not specified	COMPLETED	Opioid Use, Storage, and Disposal Among Pediatric Patients After Surgery
NCT03593720	Not specified	COMPLETED	Glans Size in Hypospadias Compared to Normal
NCT03677453	Not specified	COMPLETED	Interactive Perioperative Teaching Platform (IPTP)
NCT03685955	Not specified	WITHDRAWN	Efficacy of Amniotic Membranes in Complex Genitourinary Reconstruction
NCT03698721	Not specified	NOT_YET_RECRUITING	Urothelium Tissue Engineering Using Biopsies From Transurethral Resection of Prostate
NCT03838458	Not specified	COMPLETED	Molecular and Structural Comparison of Hypospadic and Normal Children Prepuces
NCT03911635	Not specified	UNKNOWN	Selective Criteria and a Modified Technique of Applying URAGPI Technique for More Proximal Degree of Hypospadias

Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): hypospadias