BFSP1
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
- 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:
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
- Cataract 33 (2 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 | 12 | 20 | ||||
missense | 59 | 10 | 73 | |||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 4 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 1 | |||||
splice region ? | 1 | 3 | 4 | |||
non coding ? | 23 | 33 | 57 | |||
Total | 2 | 1 | 65 | 45 | 43 |
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) | |||
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 (Jan 09, 2024) | ||
20-17494104-G-T | Cataract 33 | Benign (Dec 31, 2023) | ||
20-17494106-C-A | Inborn genetic diseases | Uncertain significance (Mar 31, 2023) | ||
20-17494129-G-A | Cataract 33 | Uncertain significance (Feb 17, 2021) | ||
20-17494133-C-G | Cataract 33 | Likely benign (Apr 10, 2023) | ||
20-17494135-A-TT | Cataract 33 | Uncertain significance (Sep 18, 2017) | ||
20-17494136-C-T | Cataract 33 | Uncertain significance (Jul 16, 2020) | ||
20-17494145-C-T | Cataract 33 • Inborn genetic diseases | Uncertain significance (Mar 19, 2024) | ||
20-17494146-G-A | not specified • Cataract 33 | Benign (Jan 27, 2024) | ||
20-17494174-G-A | Inborn genetic diseases | Uncertain significance (Feb 05, 2024) | ||
20-17494180-A-T | Uncertain significance (Apr 08, 2022) | |||
20-17494187-C-T | Inborn genetic diseases | Uncertain significance (Jul 25, 2023) | ||
20-17494188-G-A | Cataract 33 | Likely benign (Dec 07, 2023) | ||
20-17494196-C-T | Cataract 33 | Uncertain significance (Jan 22, 2024) | ||
20-17494207-A-G | Inborn genetic diseases | Uncertain significance (Apr 25, 2022) | ||
20-17494297-G-A | Cataract 33 • BFSP1-related disorder | Likely benign (Aug 10, 2023) | ||
20-17494323-T-A | Cataract 33 • BFSP1-related disorder | Benign/Likely benign (Aug 11, 2023) | ||
20-17494323-T-C | not specified • Cataract 33 | Benign (Jan 27, 2024) | ||
20-17494323-T-G | Likely benign (Oct 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) |
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