GeneBe

BFSP1

protein-coding

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

Gene summary

This gene encodes a lens-specific intermediate filament-like protein named filensin. The encoded protein is expressed in lens fiber cells after differentiation has begun. This protein functions as a component of the beaded filament which is a cytoskeletal structure found in lens fiber cells. Mutations in this gene are the cause of autosomal recessive cortical juvenile-onset cataract. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

MANE transcript

NM_001195.5

Inheritance

AR, AD, SD

ClinVar variants

P:6U:154B:51

Top phenotype

Cataract 33

gnomAD constraint

pLI —, LoF o/e 0.7

Max pathogenic AF

—

Genomic locus

chr20:17,493,905-17,569,220

External References & Databases

Ensembl (ENSG00000125864)NCBI Gene (631)OMIM (603307)HGNC:1040GenCCUniProt (Q12934)AlphaFoldClinVar (BFSP1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~75.3 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

cataract 33LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0012665

Submitter: Ambry Genetics

early-onset nuclear cataractSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0020376

Submitter: Orphanet

cataract 33STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0012665

Submitter: PanelApp Australia

cataract 33STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012665

Submitter: Labcorp Genetics (formerly Invitae)

cataract 33STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0012665

Submitter: G2P

cataract 33STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0012665

Submitter: Labcorp Genetics (formerly Invitae)

cataract 33MODERATE

Inheritance Pattern: SD

Disease ID:MONDO:0012665

Submitter: Ambry Genetics

cataract 33STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0012665

Submitter: G2P

Clinical Genomic Database (CGD)

Cataract 33AR

Manifestation: Ophthalmologic

Intervention: General

Rationale: 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

Refs: 17225135Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BFSP1 variants in ClinVar

7 Conditions Cataloged
Inborn genetic diseasesTotal: 108
Cataract 33Total: 90
not providedTotal: 61
BFSP1-related disorderTotal: 31
not specifiedTotal: 3
Congenital ocular colobomaTotal: 2
Developmental cataractTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001195.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

EffectPLPVUSLBBSum
synonymous
2
clinvar
21
clinvar
4
clinvar
 27
missense
1
clinvar
1
clinvar
135
clinvar
23
clinvar
2
clinvar
 162
nonsense
1
clinvar
3
clinvar
 4
start loss
0
frameshift
1
clinvar
1
clinvar
8
clinvar
1
clinvar
 11
splice donor/acceptor (+/-2bp)
1
clinvar
6
clinvar
 7
Total33154447211

Highest pathogenic variant AF is 0.0000065722024

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001195.5RefSeqNP_001186.18MANE Select
ENST00000377873.8EnsemblENSP00000367104.38MANE Select
NM_001161705.2RefSeqNP_001155177.18Standard
NM_001278606.2RefSeqNP_001265535.17Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

  • cytoskeleton organization
  • biological_process
  • cell maturation
  • lens fiber cell development

Molecular Function

  • structural constituent of cytoskeleton
  • structural constituent of eye lens
  • protein binding

Cellular Component

  • cytoplasm
  • intermediate filament
  • plasma membrane
  • cell cortex

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000377873
Coding exons
8
Length
75316
Individuals with no LoFs
125700
Homozygous LoFs
1
Heterozygous LoFs
47
Defined
125748
p
0.000191
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.2713043180.9570.00001784255
Missense (PolyPhen)7586.050.871591240
Synonymous1.471061270.8340.000007521337
Loss of Function1.181318.50.7047.95e-7273

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.000430.00040rare
Ashkenazi Jewish00.0absent
East Asian0.000110.00011rare
Finnish00.0absent
European (Non-Finnish)0.000250.00025rare
South Asian0.0000680.000065rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec
0.124

Intolerance Scores

LoFtool
0.372
RVIS EVS
0.04
RVIS percentile EVS
57.41

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
N
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.867

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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