BFSP1

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

Basic information

Region (hg38): 20:17493905-17569220

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
cataract 33 (Limited), mode of inheritance: AR

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.

Inborn_genetic_diseases (91 variants)
Cataract_33 (76 variants)
not_provided (50 variants)
BFSP1-related_disorder (19 variants)
Congenital_ocular_coloboma (2 variants)
Developmental_cataract (1 variants)
not_specified (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. These statistics are base on transcript: NM_000001195.5. 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			1 clinvar	17 clinvar	3 clinvar	21
missense	1 clinvar	1 clinvar	115 clinvar	19 clinvar	2 clinvar	138
nonsense	1 clinvar		2 clinvar			3
start loss						0
frameshift	1 clinvar	1 clinvar	5 clinvar		1 clinvar	8
splice donor/acceptor (+/-2bp)	2 clinvar		1 clinvar			3
Total	5	2	124	36	6

Highest pathogenic variant AF is 0.0000065722024

Loading clinvar variants...

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