FSCN3

protein-coding

fascin actin-bundling protein 3, the group of Fascin family

Gene summary

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. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_020369.3

Inheritance

—

ClinVar variants

U:78B:7

Top phenotype

Hypospadias

gnomAD constraint

pLI —, LoF o/e 0.73

Max pathogenic AF

—

Genomic locus

chr7:127,591,409-127,602,144

External References & Databases

Ensembl (ENSG00000106328)

Transcript & Mutation Effects

hg38 • Region Span ~10.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FSCN3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 83

HypospadiasTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020369.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			78 clinvar	7 clinvar		85
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	78	7	0	85

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020369.3	RefSeq	NP_065102.1	6	MANE Select
ENST00000265825.6	Ensembl	ENSP00000265825.5	6	MANE Select
ENST00000421705.1	Ensembl	ENSP00000402472.1	3	Standard
ENST00000478821.1	Ensembl	ENSP00000473531.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

establishment or maintenance of cell polarity
spermatid development
cell migration
actin filament bundle assembly

Molecular Function

protein binding, bridging
actin filament binding

Cellular Component

cytoplasm
cytoskeleton
actin cytoskeleton

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000265825
Coding exons: 6
Length: 10736
Individuals with no LoFs: 125506
Homozygous LoFs: 0
Heterozygous LoFs: 242
Defined: 125748
p: 0.000963

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.202	294	304	0.967	0.0000177	3239
Missense (PolyPhen)		70	73.862	0.94771		815
Synonymous	1.03	103	117	0.879	0.00000638	1003
Loss of Function	1.29	19	26.1	0.727	0.00000168	238

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00067	0.00067	rare
Ashkenazi Jewish	0.00089	0.00089	rare
East Asian	0.0022	0.0022	notable
Finnish	0.00028	0.00028	rare
European (Non-Finnish)	0.0012	0.0012	notable
South Asian	0.00063	0.00062	rare
Other	0.00065	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as an actin bundling protein. {ECO:0000250}.;

Intolerance Scores

LoFtool: 0.881
RVIS EVS: 0.49
RVIS percentile EVS: 79.55

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.144

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium