FSCN1

fascin actin-bundling protein 1, the group of Fascin family

Basic information

Region (hg38): 7:5592816-5606655

Previous symbols: [ "SNL" ]

Links

ENSG00000075618 ∙ NCBI:6624 ∙ OMIM:602689 ∙ HGNC:11148 ∙ Uniprot:Q16658 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FSCN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FSCN1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			37	1		38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	37	1	0

Variants in FSCN1

This is a list of pathogenic ClinVar variants found in the FSCN1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
7-5593052-G-A		not specified	Uncertain significance (Aug 20, 2024)
7-5593102-G-C		not specified	Uncertain significance (Nov 20, 2024)
7-5593130-A-C		not specified	Uncertain significance (Aug 12, 2021)
7-5593148-C-A		not specified	Uncertain significance (Sep 16, 2021)
7-5593151-C-T		not specified	Uncertain significance (Oct 16, 2024)
7-5593195-C-G		not specified	Likely benign (Feb 07, 2023)
7-5593222-C-T		not specified	Uncertain significance (Jul 02, 2024)
7-5593247-A-G		not specified	Uncertain significance (Nov 17, 2023)
7-5593255-G-A		not specified	Uncertain significance (Jan 24, 2025)
7-5593260-C-A		not specified	Uncertain significance (Oct 29, 2024)
7-5593260-C-G		not specified	Uncertain significance (May 13, 2024)
7-5593336-G-C		not specified	Uncertain significance (Feb 28, 2023)
7-5593498-G-A		not specified	Uncertain significance (Jan 24, 2024)
7-5593513-C-T		not specified	Uncertain significance (Sep 03, 2024)
7-5593558-C-T		not specified	Uncertain significance (Jul 10, 2024)
7-5593591-G-A		not specified	Uncertain significance (Aug 15, 2023)
7-5593678-G-T		not specified	Uncertain significance (Nov 10, 2024)
7-5593692-G-C		not specified	Uncertain significance (Mar 06, 2025)
7-5593710-G-C		not specified	Uncertain significance (May 20, 2024)
7-5593736-C-G		not specified	Uncertain significance (Mar 16, 2024)
7-5593738-G-A		not specified	Uncertain significance (Aug 05, 2024)
7-5593743-C-G		not specified	Uncertain significance (Dec 03, 2024)
7-5593744-G-A		not specified	Uncertain significance (Nov 17, 2022)
7-5603347-G-A		not specified	Uncertain significance (Nov 08, 2022)
7-5603371-C-T		not specified	Uncertain significance (Jan 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FSCN1	protein_coding	protein_coding	ENST00000382361	5	13848

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.869	0.131	125638	0	5	125643	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.98	224	325	0.690	0.0000190	3179
Missense in Polyphen		74	128.31	0.57672		1317
Synonymous	-0.249	153	149	1.03	0.00000993	988
Loss of Function	3.17	2	15.4	0.130	6.61e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000980	0.00000880
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Organizes filamentous actin into bundles with a minimum of 4.1:1 actin/fascin ratio. Plays a role in the organization of actin filament bundles and the formation of microspikes, membrane ruffles, and stress fibers. Important for the formation of a diverse set of cell protrusions, such as filopodia, and for cell motility and migration. {ECO:0000269|PubMed:20137952, ECO:0000269|PubMed:20393565, ECO:0000269|PubMed:9362073, ECO:0000269|PubMed:9571235}.
• Pathway: MicroRNAs in cancer - Homo sapiens (human);Interleukin-4 and 13 signaling (Consensus)

Recessive Scores

• pRec: 0.422

Intolerance Scores

• loftool: 0.0477
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.22

Haploinsufficiency Scores

• pHI: 0.213
• hipred: Y
• hipred_score: 0.825
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.918

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fscn1
• Phenotype: cellular phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; pigmentation phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; immune system phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype

Zebrafish Information Network

• Gene name: fscn1a
• Affected structure: cranial neural crest cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: cell-cell junction assembly;establishment or maintenance of cell polarity;cell population proliferation;positive regulation of lamellipodium assembly;cell migration;cytokine-mediated signaling pathway;microspike assembly;actin cytoskeleton organization;regulation of microvillus assembly;regulation of actin cytoskeleton organization;establishment of apical/basal cell polarity;cell motility;actin filament bundle assembly;positive regulation of filopodium assembly;positive regulation of podosome assembly;positive regulation of extracellular matrix disassembly
• Cellular component: stress fiber;ruffle;podosome;cytoplasm;cytosol;cytoskeleton;microvillus;cell-cell junction;actin cytoskeleton;lamellipodium;filopodium;growth cone;cell projection membrane;myelin sheath;microspike;extracellular exosome;invadopodium
• Molecular function: RNA binding;actin binding;protein binding;drug binding;protein binding, bridging;cadherin binding;actin filament binding