BEX1
Basic information
Region (hg38): X:103062651-103064171
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the BEX1 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 | 0 | |||||
| missense | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in BEX1
This is a list of pathogenic ClinVar variants found in the BEX1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| X-103062959-G-A | not specified | Uncertain significance (May 16, 2022) | ||
| X-103063067-G-A | not specified | Uncertain significance (Jan 26, 2022) | ||
| X-103063114-C-T | not specified | Uncertain significance (Apr 18, 2024) | ||
| X-103063145-A-C | not specified | Uncertain significance (Apr 01, 2024) | ||
| X-103063171-G-A | not specified | Conflicting classifications of pathogenicity (Feb 23, 2023) | ||
| X-103063180-T-C | not specified | Uncertain significance (Feb 22, 2023) | ||
| X-103063225-G-T | not specified | Uncertain significance (Sep 27, 2022) | ||
| X-103063229-T-C | not specified | Uncertain significance (Sep 06, 2022) | ||
| X-103063247-T-C | not specified | Uncertain significance (May 06, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| BEX1 | protein_coding | protein_coding | ENST00000372728 | 1 | 1590 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.543 | 0.406 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.374 | 42 | 49.4 | 0.850 | 0.00000388 | 844 |
| Missense in Polyphen | 8 | 9.7147 | 0.8235 | 211 | ||
| Synonymous | -0.915 | 21 | 16.3 | 1.29 | 0.00000113 | 218 |
| Loss of Function | 1.41 | 0 | 2.33 | 0.00 | 1.55e-7 | 43 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Signaling adapter molecule involved in p75NTR/NGFR signaling. Plays a role in cell cycle progression and neuronal differentiation. Inhibits neuronal differentiation in response to nerve growth factor (NGF). May act as a link between the cell cycle and neurotrophic factor signaling, possibly by functioning as an upstream modulator of receptor signaling, coordinating biological responses to external signals with internal cellular states (By similarity). {ECO:0000250}.;
- Pathway
- p75(NTR)-mediated signaling
(Consensus)
Recessive Scores
- pRec
- 0.431
Intolerance Scores
- loftool
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.39
Haploinsufficiency Scores
- pHI
- 0.164
- hipred
- N
- hipred_score
- 0.332
- ghis
- 0.652
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.539
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Bex2
- Phenotype
- behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); pigmentation phenotype; hematopoietic system phenotype; vision/eye phenotype; homeostasis/metabolism phenotype; immune system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype;
Gene ontology
- Biological process
- nervous system development;cell differentiation;positive regulation of transcription by RNA polymerase II;positive regulation of DNA-binding transcription factor activity
- Cellular component
- nucleus;transcription factor complex;cytoplasm
- Molecular function
- RNA polymerase II activating transcription factor binding;protein binding