BSX

Chr 11

brain specific homeobox

Also known as: BSX1

NCBI Gene: 390259ENSG00000188909UniProt: Q3C1V8OMIM: 611074

BSX encodes a DNA-binding transcription factor essential for postnatal growth, nursing behavior, and energy balance regulation through control of neuropeptide Y and agouti-related peptide neuronal function. Mutations cause neurodevelopmental disorders affecting growth and feeding behaviors, with autosomal recessive inheritance patterns reported. The gene shows relatively low constraint against loss-of-function variants, suggesting tolerance to heterozygous disruption.

OMIMResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 1.33
Clinical Summary— BSX
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
49 unique Pathogenic / Likely Pathogenic· 27 VUS of 80 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.33LOEUF
pLI 0.008
Z-score 1.01
OE 0.58 (0.29–1.33)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.48Z-score
OE missense 0.88 (0.76–1.03)
115 obs / 130.6 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.58 (0.29–1.33)
0≤0.351.4
Missense OE0.88 (0.76–1.03)
0≤0.61.4
Synonymous OE1.06
0≤1.21.6
LoF obs/exp: 4 / 6.8Missense obs/exp: 115 / 130.6Syn Z: -0.35
DN
0.7036th %ile
GOF
0.4678th %ile
LOF
0.54top 25%

The highest-scoring mechanism for this gene is dominant-negative.

DNprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

80 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic47
Likely Pathogenic2
VUS27
Likely Benign1
Benign3
47
Pathogenic
2
Likely Pathogenic
27
VUS
1
Likely Benign
3
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
47
0
47
Likely Pathogenic
0
0
2
0
2
VUS
0
24
3
0
27
Likely Benign
0
0
0
1
1
Benign
0
1
0
2
3
Total02552380

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

BSX · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
[Meta analysis of clinical safety and efficacy evaluation of peripheral arterial disease patients with critical limb ischemia who accepted bypass surgery or endovascular therapy].
Shen SK et al.·Zhonghua Yi Xue Za Zhi
2017Meta-analysis
Single-center thorough evaluation and targeted treatment of globozoospermic men.
Cheung S et al.·J Assist Reprod Genet
2021Clinical trial
Treatment Outcomes in Octogenarians with Chronic Limb-Threatening Ischemia after Infrainguinal Bypass Surgery or Endovascular Therapy.
Morisaki K et al.·Ann Vasc Surg
2024
Immune Deficiency in Jacobsen Syndrome: Molecular and Phenotypic Characterization.
Rodríguez-López R et al.·Genes (Basel)
2021Case report
Bypass Surgery vs. Drug-Eluting Stent for Trans-Atlantic Inter-Society Consensus-II (TASCII) C or D Femoropopliteal Lesions.
Soga Y et al.·Circ J
2015Clinical trial
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Genetic ablation of the Bsx homeodomain transcription factor in zebrafish: Impact on mature pineal gland morphology and circadian behavior.
Carstensen MB et al.·J Pineal Res
2022Open AccessFunctional
Possible role of transcription factors (BSX, NKX2.1, IRX3 and SIRT1) in the regulation of appetite in goldfish (Carassius auratus).
Vinnicombe KRT et al.·Comp Biochem Physiol A Mol Integr Physiol
2022
Bsx Is Essential for Differentiation of Multiple Neuromodulatory Cell Populations in the Secondary Prosencephalon.
Schredelseker T et al.·Front Neurosci
2020Open Access
Circadian regulation and molecular role of the Bsx homeobox gene in the adult pineal gland.
Carstensen MB et al.·J Pineal Res
2020
Brain-specific homeobox Bsx specifies identity of pineal gland between serially homologous photoreceptive organs in zebrafish.
Mano H et al.·Commun Biol
2019Open AccessFunctional
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients