BSX
protein-codingbrain specific homeobox, the group of NKL subclass homeoboxes and pseudogenes
Gene summary
Enables sequence-specific double-stranded DNA binding activity. Predicted to be involved in several processes, including eating behavior; regulation of transcription by RNA polymerase II; and stem cell population maintenance. Predicted to act upstream of or within locomotory behavior; mammary gland involution; and positive regulation of transcription by RNA polymerase II. Predicted to be located in chromatin and cytoplasm. Predicted to be part of transcription regulator complex. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~4.3 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 BSX variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001098169.2. 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 | 2 | 3 | |||
| missense | 25 | 1 | 26 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 25 | 1 | 3 | 29 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001091639.1 | 3 | MANE Select | |
| Ensembl | ENSP00000344285.2 | 3 | MANE Select |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| bsx | Danio rerio | Structure: pinealocyte Quality: decreased occurrence abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of transcription by RNA polymerase II
- locomotory behavior
- eating behavior
- positive regulation of transcription by RNA polymerase II
- mammary gland involution
Molecular Function
- RNA polymerase II proximal promoter sequence-specific DNA binding
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA-binding transcription factor activity
- sequence-specific DNA binding
Cellular Component
- nucleus
- transcription factor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000343035
- Coding exons
- 3
- Length
- 4151
- Individuals with no LoFs
- 124613
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 180
- Defined
- 124793
- p
- 0.000721
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.484 | 115 | 131 | 0.881 | 0.00000603 | 1466 |
| Missense (PolyPhen) | 23 | 36.511 | 0.62995 | 416 | ||
| Synonymous | -0.351 | 62 | 58.6 | 1.06 | 0.00000279 | 500 |
| Loss of Function | 1.01 | 4 | 6.85 | 0.584 | 2.99e-7 | 80 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0021 | 0.0016 | notable |
| Latino/Admixed American | 0.00026 | 0.00023 | rare |
| Ashkenazi Jewish | 0.00055 | 0.00050 | rare |
| East Asian | 0.00019 | 0.00017 | rare |
| Finnish | 0.0012 | 0.0010 | notable |
| European (Non-Finnish) | 0.0011 | 0.00088 | notable |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.0025 | 0.0021 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: DNA binding protein that function as transcriptional activator. Is essential for normal postnatal growth and nursing. Is an essential factor for neuronal neuropeptide Y and agouti- related peptide function and locomotory behavior in the control of energy balance (By similarity). {ECO:0000250}.;
Intolerance Scores
- LoFtool
- 0.361
- RVIS EVS
- 0.17
- RVIS percentile EVS
- 65.56
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.435
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |