BEX3
protein-codingbrain expressed X-linked 3, the group of Brain expressed X-linked family
Gene summary
Enables identical protein binding activity. Predicted to be involved in negative regulation of protein ubiquitination and signal transduction. Predicted to act upstream of or within extrinsic apoptotic signaling pathway via death domain receptors. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]
- NGFRAP1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~1.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BEX3 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_206917.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | 2 | |||
| missense | 0 | |||||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 2 | 1 | 0 | 3 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_996800.1 | 1 | MANE Select | |
| Ensembl | ENSP00000354843.4 | 1 | MANE Select | |
| RefSeq | NP_001269603.1 | 2 | Standard | |
| RefSeq | NP_055195.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neurotrophin signaling pathway - Homo sapiens (human)
- Apoptosis-related network due to altered Notch3 in ovarian cancer
- Signal Transduction
- NADE modulates death signalling
- Death Receptor Signalling
Biological Process
- activation of cysteine-type endopeptidase activity involved in apoptotic process
- multicellular organism development
- extrinsic apoptotic signaling pathway via death domain receptors
- negative regulation of cysteine-type endopeptidase activity involved in apoptotic process
- regulation of cysteine-type endopeptidase activity involved in apoptotic process
Molecular Function
- nerve growth factor receptor binding
- protein binding
- cysteine-type endopeptidase activator activity involved in apoptotic process
- identical protein binding
- metal ion binding
Cellular Component
- nucleus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000372645
- Coding exons
- 1
- Length
- 1738
- Individuals with no LoFs
- 0
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 0
- Defined
- 0
- p
- 0.00
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.995 | 28 | 47.2 | 0.593 | 0.00000352 | 748 |
| Missense (PolyPhen) | 3 | 11.083 | 0.27067 | 223 | ||
| Synonymous | -0.757 | 17 | 13.5 | 1.26 | 8.64e-7 | 197 |
| Loss of Function | 1.63 | 0 | 3.09 | 0.00 | 2.78e-7 | 37 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be a signaling adapter molecule involved in p75NTR- mediated apoptosis induced by NGF. Plays a role in zinc-triggered neuronal death (By similarity). May play an important role in the pathogenesis of neurogenetic diseases. {ECO:0000250}.;
Intolerance Scores
- RVIS EVS
- -0.01
- RVIS percentile EVS
- 52.85
Essentials
- Essential (gene trap)
- N