BFSP1

beaded filament structural protein 1, the group of Beaded filament structural proteins

Basic information

Region (hg38): 20:17493904-17569220

Links

ENSG00000125864 ∙ NCBI:631 ∙ OMIM:603307 ∙ HGNC:1040 ∙ Uniprot:Q12934 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cataract 33 (Moderate), mode of inheritance: Semidominant
• early-onset nuclear cataract (Supportive), mode of inheritance: AD
• cataract 33 (Strong), mode of inheritance: AR
• cataract 33 (Strong), mode of inheritance: AD
• cataract 33 (Strong), mode of inheritance: AR
• cataract 33 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cataract 33	AR	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	17225135

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BFSP1 gene.

• not provided (72 variants)
• Cataract 33 (59 variants)
• Inborn genetic diseases (29 variants)
• not specified (6 variants)
• Congenital ocular coloboma (1 variants)
• - (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BFSP1 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			1	8	8	17
missense		1	43	8	3	55
nonsense	1					1
start loss						0
frameshift	1		3			4
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1	2		3
non coding			1	22	33	56
Total	2	1	49	38	44

Highest pathogenic variant AF is 0.00000657

Variants in BFSP1

This is a list of pathogenic ClinVar variants found in the BFSP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-17493942-G-A			Likely benign (Jul 21, 2018)
20-17494045-T-G			Benign (Jun 29, 2018)
20-17494065-C-G			Benign (May 17, 2018)
20-17494075-TAA-T		Congenital ocular coloboma • Cataract 33	Benign (Jan 09, 2024)
20-17494104-G-T		Cataract 33	Benign (Dec 31, 2023)
20-17494106-C-A		Inborn genetic diseases	Uncertain significance (Mar 31, 2023)
20-17494129-G-A		Cataract 33	Uncertain significance (Feb 17, 2021)
20-17494133-C-G		Cataract 33	Likely benign (Apr 10, 2023)
20-17494135-A-TT		Cataract 33	Uncertain significance (Sep 18, 2017)
20-17494136-C-T		Cataract 33	Uncertain significance (Jul 16, 2020)
20-17494145-C-T		Cataract 33	Uncertain significance (Dec 09, 2023)
20-17494146-G-A		not specified • Cataract 33	Benign (Jan 27, 2024)
20-17494174-G-A		Inborn genetic diseases	Uncertain significance (Feb 05, 2024)
20-17494180-A-T			Uncertain significance (Apr 08, 2022)
20-17494187-C-T		Inborn genetic diseases	Uncertain significance (Jul 25, 2023)
20-17494188-G-A		Cataract 33	Likely benign (Dec 07, 2023)
20-17494196-C-T		Cataract 33	Uncertain significance (Jan 22, 2024)
20-17494207-A-G		Inborn genetic diseases	Uncertain significance (Apr 25, 2022)
20-17494297-G-A		Cataract 33 • BFSP1-related disorder	Likely benign (Aug 10, 2023)
20-17494323-T-A		Cataract 33 • BFSP1-related disorder	Benign/Likely benign (Aug 11, 2023)
20-17494323-T-C		not specified • Cataract 33	Benign (Jan 27, 2024)
20-17494323-T-G			Likely benign (Oct 01, 2022)
20-17494336-C-G		Inborn genetic diseases	Uncertain significance (Jun 03, 2022)
20-17494368-C-A		Inborn genetic diseases	Uncertain significance (Jun 28, 2023)
20-17494378-C-T		Inborn genetic diseases	Likely benign (Mar 24, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BFSP1	protein_coding	protein_coding	ENST00000377873	8	75316

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.85e-7	0.675	125700	1	47	125748	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.271	304	318	0.957	0.0000178	4255
Missense in Polyphen		75	86.05	0.87159		1240
Synonymous	1.47	106	127	0.834	0.00000752	1337
Loss of Function	1.18	13	18.5	0.704	7.95e-7	273

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000434	0.000434
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000246	0.000246
Middle Eastern	0.000109	0.000109
South Asian	0.0000681	0.0000653
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.124

Intolerance Scores

• loftool: 0.372
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.41

Haploinsufficiency Scores

• pHI: 0.161
• hipred: N
• hipred_score: 0.456
• ghis: 0.468

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.867

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Bfsp1
• Phenotype: vision/eye phenotype

Gene ontology

• Biological process: cytoskeleton organization;biological_process;cell maturation;lens fiber cell development
• Cellular component: cytoplasm;intermediate filament;plasma membrane;cell cortex
• Molecular function: structural constituent of cytoskeleton;structural constituent of eye lens;protein binding