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GeneBe

BFSP1

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

Basic information

Region (hg38): 20:17493904-17569220

Links

ENSG00000125864NCBI:631OMIM:603307HGNC:1040Uniprot:Q12934AlphaFoldGenCCjaxSfariGnomADPubmed

Phenotypes

GenCC

Source: genCC

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

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Cataract 33ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic17225135

ClinVar

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

  • not provided (76 variants)
  • Cataract 33 (58 variants)
  • Inborn genetic diseases (13 variants)
  • not specified (6 variants)
  • Congenital ocular coloboma (2 variants)
  • Developmental cataract (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.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous 1 5 8 14
missense 1 1 30 8 4 44
nonsense 1 1 1 3
start loss 0
frameshift 1 1 2
inframe indel 1 1
splice variant 1 2 2 5
non coding 1 23 33 57
Total 4 2 35 39 46

Highest pathogenic variant AF is 0.00000657

Variants in BFSP1

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

Position Type Phenotype Significance ClinVar
20-17493942-G-A Likely benign (Jul 21, 2018)link
20-17494045-T-G Benign (Jun 29, 2018)link
20-17494065-C-G Benign (May 17, 2018)link
20-17494075-TAA-T Congenital ocular coloboma • Cataract 33 Benign (Aug 23, 2022)link
20-17494104-G-T Cataract 33 Benign (Oct 17, 2022)link
20-17494106-C-A Inborn genetic diseases Uncertain significance (Mar 31, 2023)link
20-17494129-G-A Cataract 33 Uncertain significance (Aug 24, 2021)link
20-17494133-C-G Cataract 33 Likely benign (Dec 13, 2017)link
20-17494135-A-TT Cataract 33 Uncertain significance (Sep 18, 2017)link
20-17494136-C-T Cataract 33 Uncertain significance (Sep 01, 2021)link
20-17494146-G-A not specified • Cataract 33 Benign (Nov 01, 2022)link
20-17494180-A-T Uncertain significance (Apr 08, 2022)link
20-17494187-C-T Inborn genetic diseases Uncertain significance (Jul 25, 2023)link
20-17494207-A-G Inborn genetic diseases Uncertain significance (Apr 25, 2022)link
20-17494297-G-A Cataract 33 Likely benign (Apr 18, 2022)link
20-17494323-T-A Cataract 33 Benign (Mar 26, 2021)link
20-17494323-T-C not specified • Cataract 33 Benign (Nov 01, 2022)link
20-17494336-C-G Inborn genetic diseases Uncertain significance (Jun 03, 2022)link
20-17494368-C-A Inborn genetic diseases Uncertain significance (Jun 28, 2023)link
20-17494378-C-T Inborn genetic diseases Likely benign (Mar 24, 2023)link
20-17494393-C-T Uncertain significance (-)link
20-17494562-C-T Inborn genetic diseases Uncertain significance (Feb 14, 2023)link
20-17494572-C-T not specified • Cataract 33 Benign (Nov 01, 2022)link
20-17494579-GA-G - no interpretation for the single variant (-)link
20-17494604-T-C Cataract 33 Uncertain significance (Aug 27, 2021)link

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BFSP1protein_codingprotein_codingENST00000377873 875316
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.85e-70.6751257001471257480.000191
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2713043180.9570.00001784255
Missense in Polyphen7586.050.871591240
Synonymous1.471061270.8340.000007521337
Loss of Function1.181318.50.7047.95e-7273

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0004340.000434
Ashkenazi Jewish0.000.00
East Asian0.0001090.000109
Finnish0.000.00
European (Non-Finnish)0.0002460.000246
Middle Eastern0.0001090.000109
South Asian0.00006810.0000653
Other0.0003260.000326

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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