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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:Q12934AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

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 (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
clinvar
8
clinvar
8
clinvar
17
missense
1
clinvar
43
clinvar
8
clinvar
3
clinvar
55
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
3
clinvar
4
inframe indel
0
splice donor/acceptor (+/-2bp)
1
clinvar
1
splice region
1
2
3
non coding
1
clinvar
22
clinvar
33
clinvar
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)1213460
20-17494045-T-G Benign (Jun 29, 2018)1283614
20-17494065-C-G Benign (May 17, 2018)1285829
20-17494075-TAA-T Congenital ocular coloboma • Cataract 33 Benign (Jan 09, 2024)68470
20-17494104-G-T Cataract 33 Benign (Dec 31, 2023)702116
20-17494106-C-A Inborn genetic diseases Uncertain significance (Mar 31, 2023)2523332
20-17494129-G-A Cataract 33 Uncertain significance (Feb 17, 2021)1497022
20-17494133-C-G Cataract 33 Likely benign (Apr 10, 2023)541143
20-17494135-A-TT Cataract 33 Uncertain significance (Sep 18, 2017)541141
20-17494136-C-T Cataract 33 Uncertain significance (Jul 16, 2020)570329
20-17494145-C-T Cataract 33 Uncertain significance (Dec 09, 2023)2895983
20-17494146-G-A not specified • Cataract 33 Benign (Jan 27, 2024)257616
20-17494174-G-A Inborn genetic diseases Uncertain significance (Feb 05, 2024)3133781
20-17494180-A-T Uncertain significance (Apr 08, 2022)1804600
20-17494187-C-T Inborn genetic diseases Uncertain significance (Jul 25, 2023)2600820
20-17494188-G-A Cataract 33 Likely benign (Dec 07, 2023)2719201
20-17494196-C-T Cataract 33 Uncertain significance (Jan 22, 2024)2849469
20-17494207-A-G Inborn genetic diseases Uncertain significance (Apr 25, 2022)2285533
20-17494297-G-A Cataract 33 • BFSP1-related condition Likely benign (Aug 10, 2023)474090
20-17494323-T-A Cataract 33 • BFSP1-related condition Benign/Likely benign (Aug 11, 2023)1166147
20-17494323-T-C not specified • Cataract 33 Benign (Jan 27, 2024)257615
20-17494323-T-G Likely benign (Oct 01, 2022)2652210
20-17494336-C-G Inborn genetic diseases Uncertain significance (Jun 03, 2022)2346635
20-17494368-C-A Inborn genetic diseases Uncertain significance (Jun 28, 2023)2606998
20-17494378-C-T Inborn genetic diseases Likely benign (Mar 24, 2023)2529822

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