FSCN2

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

Basic information

Region (hg38): 17:81528376-81537130

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 (543 variants)
• Inborn genetic diseases (52 variants)
• not specified (19 variants)
• Retinitis pigmentosa 30 (14 variants)
• Macular degeneration (1 variants)
• Leber congenital amaurosis (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.

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			2	125	15	142
missense			289	8	4	301
nonsense			10			10
start loss						0
frameshift			12		1	13
inframe indel			7			7
splice donor/acceptor (+/-2bp)			2	1		3
splice region			3	10	1	14
non coding			15	39		54
Total	0	0	337	173	20

Variants in FSCN2

This is a list of pathogenic ClinVar variants found in the FSCN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-81528536-C-T			Uncertain significance (Oct 13, 2023)
17-81528537-G-A			Likely benign (Aug 23, 2021)
17-81528539-C-T			Uncertain significance (Apr 11, 2022)
17-81528540-G-A			Likely benign (Dec 29, 2022)
17-81528543-C-T			Likely benign (Jun 13, 2022)
17-81528544-G-A			Uncertain significance (Sep 11, 2023)
17-81528545-G-T			Uncertain significance (Mar 19, 2022)
17-81528546-C-T			Likely benign (Sep 22, 2022)
17-81528547-C-A			Uncertain significance (Sep 01, 2022)
17-81528550-C-T			Uncertain significance (Dec 11, 2023)
17-81528553-C-T		Retinal dystrophy	Likely pathogenic (Oct 01, 2023)
17-81528556-G-T			Uncertain significance (Jan 29, 2024)
17-81528560-T-C			Uncertain significance (Sep 19, 2022)
17-81528561-G-A			Likely benign (Oct 15, 2023)
17-81528564-G-A			Likely benign (Jul 06, 2022)
17-81528573-T-G			Uncertain significance (Feb 04, 2021)
17-81528576-C-T			Likely benign (Nov 27, 2023)
17-81528579-C-T		not specified	Benign/Likely benign (Jan 18, 2024)
17-81528580-G-A		Retinitis pigmentosa 30 • not specified	Likely benign (Jan 25, 2024)
17-81528583-A-G			Uncertain significance (May 10, 2022)
17-81528585-C-T		Retinal dystrophy	Conflicting classifications of pathogenicity (Oct 01, 2023)
17-81528586-G-A			Uncertain significance (Nov 27, 2023)
17-81528586-G-C			Uncertain significance (Jan 27, 2022)
17-81528587-A-T		not specified	Uncertain significance (Mar 01, 2024)
17-81528595-C-T			Uncertain significance (Oct 24, 2022)

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