BFSP1
beaded filament structural protein 1, the group of Beaded filament structural proteins
Basic information
Region (hg38): 20:17493904-17569220
Links
Phenotypes
GenCC
Source:
- cataract 33 (Moderate), mode of inheritance: Semidominant
- early-onset nuclear cataract (Supportive), mode of inheritance: AD
Clinical Genomic Database
Source:
| 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
- 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) | |||
| 20-17494045-T-G | Benign (Jun 29, 2018) | |||
| 20-17494065-C-G | Benign (May 17, 2018) | |||
| 20-17494075-TAA-T | Congenital ocular coloboma • Cataract 33 | Benign (Aug 23, 2022) | ||
| 20-17494104-G-T | Cataract 33 | Benign (Oct 17, 2022) | ||
| 20-17494106-C-A | Inborn genetic diseases | Uncertain significance (Mar 31, 2023) | ||
| 20-17494129-G-A | Cataract 33 | Uncertain significance (Aug 24, 2021) | ||
| 20-17494133-C-G | Cataract 33 | Likely benign (Dec 13, 2017) | ||
| 20-17494135-A-TT | Cataract 33 | Uncertain significance (Sep 18, 2017) | ||
| 20-17494136-C-T | Cataract 33 | Uncertain significance (Sep 01, 2021) | ||
| 20-17494146-G-A | not specified • Cataract 33 | Benign (Nov 01, 2022) | ||
| 20-17494180-A-T | Uncertain significance (Apr 08, 2022) | |||
| 20-17494187-C-T | Inborn genetic diseases | Uncertain significance (Jul 25, 2023) | ||
| 20-17494207-A-G | Inborn genetic diseases | Uncertain significance (Apr 25, 2022) | ||
| 20-17494297-G-A | Cataract 33 | Likely benign (Apr 18, 2022) | ||
| 20-17494323-T-A | Cataract 33 | Benign (Mar 26, 2021) | ||
| 20-17494323-T-C | not specified • Cataract 33 | Benign (Nov 01, 2022) | ||
| 20-17494336-C-G | Inborn genetic diseases | Uncertain significance (Jun 03, 2022) | ||
| 20-17494368-C-A | Inborn genetic diseases | Uncertain significance (Jun 28, 2023) | ||
| 20-17494378-C-T | Inborn genetic diseases | Likely benign (Mar 24, 2023) | ||
| 20-17494393-C-T | Uncertain significance (-) | |||
| 20-17494562-C-T | Inborn genetic diseases | Uncertain significance (Feb 14, 2023) | ||
| 20-17494572-C-T | not specified • Cataract 33 | Benign (Nov 01, 2022) | ||
| 20-17494579-GA-G | - | no interpretation for the single variant (-) | ||
| 20-17494604-T-C | Cataract 33 | Uncertain significance (Aug 27, 2021) |
GnomAD
Source:
| 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:
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