FSCN3

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

Basic information

Region (hg38): 7:127591408-127602144

Links

ENSG00000106328 ∙ NCBI:29999 ∙ OMIM:615800 ∙ HGNC:3961 ∙ Uniprot:Q9NQT6 ∙ 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 FSCN3 gene.

• Inborn genetic diseases (25 variants)
• Hypospadias (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FSCN3 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			23	3		26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	3	0

Variants in FSCN3

This is a list of pathogenic ClinVar variants found in the FSCN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-127593864-C-T		not specified	Uncertain significance (May 04, 2023)
7-127595349-G-A		not specified	Uncertain significance (Sep 16, 2021)
7-127595359-T-C		not specified	Uncertain significance (Oct 25, 2022)
7-127595454-C-T		not specified	Uncertain significance (Mar 16, 2022)
7-127595463-C-T		not specified	Uncertain significance (Dec 20, 2021)
7-127595529-G-A		not specified	Uncertain significance (Dec 13, 2022)
7-127595560-A-G		not specified	Uncertain significance (Mar 25, 2022)
7-127595566-T-A		not specified	Uncertain significance (Nov 29, 2021)
7-127595622-C-T		not specified	Uncertain significance (Nov 30, 2022)
7-127595655-C-G		not specified	Uncertain significance (Dec 28, 2023)
7-127595655-C-T		not specified	Uncertain significance (Apr 06, 2023)
7-127595656-G-A		not specified	Uncertain significance (Feb 08, 2023)
7-127595670-G-A		not specified	Uncertain significance (Feb 22, 2023)
7-127595673-G-A		not specified	Uncertain significance (Nov 07, 2022)
7-127595685-C-G		not specified	Uncertain significance (Feb 17, 2024)
7-127595691-G-A		not specified	Uncertain significance (May 30, 2023)
7-127595716-G-A		not specified	Likely benign (Jul 26, 2022)
7-127595766-G-A		not specified	Uncertain significance (Sep 29, 2022)
7-127595772-C-T		not specified	Uncertain significance (Oct 05, 2023)
7-127595773-G-A		not specified	Uncertain significance (Oct 04, 2022)
7-127595820-C-T		not specified	Uncertain significance (Dec 28, 2022)
7-127595848-A-T		not specified	Uncertain significance (Feb 17, 2024)
7-127595945-C-A		not specified	Uncertain significance (Nov 13, 2023)
7-127595968-G-A		not specified	Likely benign (Dec 03, 2021)
7-127595983-G-A		not specified	Uncertain significance (Jan 02, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FSCN3	protein_coding	protein_coding	ENST00000265825	6	10736

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.35e-10	0.556	125506	0	242	125748	0.000963

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.202	294	304	0.967	0.0000177	3239
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000974	0.000974
Ashkenazi Jewish	0.000894	0.000893
East Asian	0.00223	0.00223
Finnish	0.000277	0.000277
European (Non-Finnish)	0.00119	0.00119
Middle Eastern	0.00223	0.00223
South Asian	0.000629	0.000621
Other	0.000653	0.000652

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.144
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.144

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fscn3

Gene ontology

• Biological process: establishment or maintenance of cell polarity;spermatid development;cell migration;actin filament bundle assembly
• Cellular component: cytoplasm;cytoskeleton;actin cytoskeleton
• Molecular function: protein binding, bridging;actin filament binding