FSCN2

fascin actin-bundling protein 2, retinal, the group of Fascin family

Basic information

Region (hg38): 17:81528377-81537130

Links

ENSG00000186765

∙ NCBI:25794 ∙ OMIM:607643 ∙ HGNC:3960 ∙ Uniprot:O14926 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

retinitis pigmentosa (Supportive), mode of inheritance: AD
retinitis pigmentosa 30 (Disputed Evidence), mode of inheritance: AD
retinitis pigmentosa 30 (Limited), mode of inheritance: AD
retinitis pigmentosa 30 (Limited), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Retinitis pigmentosa 30	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	11527955

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the FSCN2 gene.

not_provided (631 variants)
not_specified (160 variants)
Retinal_dystrophy (41 variants)
Retinitis_pigmentosa_30 (17 variants)
FSCN2-related_disorder (16 variants)
Meniere_disease (4 variants)
Leber_congenital_amaurosis (1 variants)
Macular_degeneration (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FSCN2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000012418.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			4 clinvar	162 clinvar	12 clinvar	178
missense		1 clinvar	358 clinvar	27 clinvar	3 clinvar	389
nonsense		1 clinvar	10 clinvar			11
start loss						0
frameshift		1 clinvar	14 clinvar	1 clinvar		16
splice donor/acceptor (+/-2bp)			5 clinvar	1 clinvar	1 clinvar	7
Total	0	3	391	191	16

Highest pathogenic variant AF is 7.3982994e-7

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FSCN2	protein_coding	protein_coding	ENST00000334850	5	8735

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.83e-13	0.0242	123656	1	330	123987	0.00134

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.114	344	338	1.02	0.0000243	3251
Missense in Polyphen		138	144.8	0.95302		1466
Synonymous	-1.82	175	147	1.19	0.0000109	1070
Loss of Function	-0.0364	19	18.8	1.01	0.00000109	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000926	0.000920
Ashkenazi Jewish	0.000734	0.000700
East Asian	0.0123	0.0120
Finnish	0.000159	0.000139
European (Non-Finnish)	0.000566	0.000500
Middle Eastern	0.0123	0.0120
South Asian	0.000596	0.000556
Other	0.000882	0.000830

dbNSFP

Source: dbNSFP

Function: FUNCTION: Acts as an actin bundling protein. May play a pivotal role in photoreceptor cell-specific events, such as disk morphogenesis.;

Recessive Scores

pRec: 0.143

Haploinsufficiency Scores

pHI: 0.0919
hipred: N
hipred_score: 0.275
ghis: 0.502

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.510

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Fscn2
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); hearing/vestibular/ear phenotype; vision/eye phenotype;

Gene ontology

Biological process: establishment or maintenance of cell polarity;visual perception;anatomical structure morphogenesis;cell migration;actin cytoskeleton organization;eye photoreceptor cell development;actin filament bundle assembly
Cellular component: cytoplasm;actin cytoskeleton;stereocilium
Molecular function: actin binding;protein binding, bridging;actin filament binding