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GeneBe

BFSP2

beaded filament structural protein 2, the group of Beaded filament structural proteins

Basic information

Region (hg38): 3:133400055-133475222

Links

ENSG00000170819NCBI:8419OMIM:603212HGNC:1041Uniprot:Q13515AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • cataract 12 multiple types (Definitive), mode of inheritance: AD
  • pulverulent cataract (Supportive), mode of inheritance: AD
  • early-onset sutural cataract (Supportive), mode of inheritance: AD
  • early-onset lamellar cataract (Supportive), mode of inheritance: AD
  • cataract 12 multiple types (Definitive), mode of inheritance: AR
  • cataract 12 multiple types (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Cataract 12, multiple typesAD/ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingOphthalmologic10729115; 10739768; 10634598; 15570218; 17982427; 18958306; 21836522

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BFSP2 gene.

  • Cataract 12 multiple types (60 variants)
  • not provided (38 variants)
  • Inborn genetic diseases (23 variants)
  • BFSP2-related condition (2 variants)
  • Cataract (1 variants)
  • not specified (1 variants)
  • 7 conditions (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BFSP2 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
3
clinvar
5
clinvar
8
clinvar
16
missense
35
clinvar
5
clinvar
4
clinvar
44
nonsense
1
clinvar
1
clinvar
2
start loss
0
frameshift
1
clinvar
2
clinvar
3
inframe indel
1
clinvar
1
clinvar
2
splice donor/acceptor (+/-2bp)
0
splice region
?
2
2
4
non coding
?
4
clinvar
14
clinvar
19
clinvar
37
Total 3 0 46 24 31

Variants in BFSP2

This is a list of pathogenic ClinVar variants found in the BFSP2 region.

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

Position Type Phenotype Significance ClinVar
3-133400080-G-A Cataract 12 multiple types Likely benign (Jan 13, 2018)900394
3-133400088-G-A Cataract 12 multiple types Uncertain significance (Jan 13, 2018)343397
3-133400096-C-T Cataract 12 multiple types Uncertain significance (May 14, 2018)1031336
3-133400107-G-A Cataract 12 multiple types Likely benign (Apr 18, 2019)1118999
3-133400110-C-G Cataract 12 multiple types Uncertain significance (May 03, 2021)2439510
3-133400134-C-T Cataract 12 multiple types Likely benign (Nov 30, 2021)1556763
3-133400158-G-A Cataract 12 multiple types Benign (Jun 20, 2022)343398
3-133400183-T-C Cataract 12 multiple types Benign (Jan 12, 2018)343399
3-133400213-A-G Inborn genetic diseases Uncertain significance (Aug 10, 2023)2617661
3-133400238-G-A Inborn genetic diseases Uncertain significance (Jul 11, 2023)1306035
3-133400245-C-T Cataract 12 multiple types Benign (Sep 27, 2022)343400
3-133400245-CG-C Cataract 12 multiple types Pathogenic (Sep 06, 2022)646545
3-133400246-G-A Inborn genetic diseases Likely benign (Oct 03, 2022)2315690
3-133400273-G-T Cataract 12 multiple types Uncertain significance (Jul 26, 2022)2413884
3-133400279-A-G Inborn genetic diseases Uncertain significance (Mar 01, 2023)2465893
3-133400298-G-A Cataract 12 multiple types Uncertain significance (Oct 31, 2022)2715249
3-133400310-G-A Inborn genetic diseases Uncertain significance (Mar 29, 2023)2569163
3-133400315-C-A Inborn genetic diseases Uncertain significance (Sep 17, 2021)2251242
3-133400318-G-A Inborn genetic diseases Uncertain significance (Oct 03, 2022)2411327
3-133400329-T-C Cataract 12 multiple types Benign (Dec 10, 2021)343401
3-133400332-C-CT Cataract 12 multiple types Uncertain significance (Apr 28, 2017)343402
3-133400337-T-A Inborn genetic diseases Uncertain significance (Jul 05, 2023)2600571
3-133400345-C-A Inborn genetic diseases Uncertain significance (Oct 21, 2021)2256244
3-133400348-C-T Developmental cataract Uncertain significance (May 01, 2021)1065595
3-133400368-C-T Cataract 12 multiple types Benign (Jan 13, 2018)900455

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
BFSP2protein_codingprotein_codingENST00000302334 775228
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.22e-80.7721256980501257480.000199
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.2922392520.9480.00001612683
Missense in Polyphen6463.9141.0013770
Synonymous0.9178899.60.8830.00000613855
Loss of Function1.421522.30.6740.00000138218

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002680.000268
Ashkenazi Jewish0.0001990.000198
East Asian0.0002720.000272
Finnish0.0003050.000277
European (Non-Finnish)0.0001950.000185
Middle Eastern0.0002720.000272
South Asian0.0002610.000261
Other0.0001640.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Involved in stabilization of lens fiber cell cytoskeleton. {ECO:0000250|UniProtKB:Q6NVD9}.;

Recessive Scores

pRec
0.113

Intolerance Scores

loftool
0.218
rvis_EVS
-0.38
rvis_percentile_EVS
27.88

Haploinsufficiency Scores

pHI
0.335
hipred
N
hipred_score
0.237
ghis
0.416

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.0918

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Bfsp2
Phenotype
vision/eye phenotype; cellular phenotype;

Gene ontology

Biological process
visual perception;intermediate filament cytoskeleton organization;cell maturation;response to stimulus;lens fiber cell development
Cellular component
intermediate filament;plasma membrane;cell cortex
Molecular function
structural constituent of cytoskeleton;structural constituent of eye lens;protein binding