BEND5

Chr 1

BEN domain containing 5

Also known as: C1orf165

NCBI Gene: 79656ENSG00000162373UniProt: Q7L4P6OMIM: 621198

This protein acts as a transcriptional repressor that binds DNA and negatively regulates gene transcription. Mutations in BEND5 have not been definitively associated with human disease, though the gene shows moderate constraint against loss-of-function variants. The protein is predicted to localize to the Golgi apparatus in addition to its nuclear transcriptional regulatory functions.

OMIMResearchSummary from RefSeq, UniProt
DNmechanismLOEUF 0.66
Clinical Summary— BEND5
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.31) despite low pLI — interpret in context.
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
0.66LOEUF
pLI 0.054
Z-score 2.54
OE 0.31 (0.16–0.66)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
1.70Z-score
OE missense 0.68 (0.59–0.78)
152 obs / 223.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.31 (0.16–0.66)
0≤0.351.4
Missense OE0.68 (0.59–0.78)
0≤0.61.4
Synonymous OE1.07
0≤1.21.6
LoF obs/exp: 5 / 16.0Missense obs/exp: 152 / 223.7Syn Z: -0.54
DN
0.6258th %ile
GOF
0.4480th %ile
LOF
0.4332th %ile

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

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

BEND5 · 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.

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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
Interaction between BEND5 and RBPJ suppresses breast cancer growth and metastasis via inhibiting Notch signaling.
Shi Y et al.·Int J Biol Sci
2022
HIF-1α is involved in blood-brain barrier dysfunction and paracellular migration of bacteria in pneumococcal meningitis.
Devraj G et al.·Acta Neuropathol
2020
The Diagnostic Value of Pan-Trk Expression to Detect Neurotrophic Tyrosine Receptor Kinase (NTRK) Gene Fusion in CNS Tumours: A Study Using Next-Generation Sequencing Platform.
Mohamed F et al.·Pathol Oncol Res
2022
Genomic Profiling of a Large Set of Diverse Pediatric Cancers Identifies Known and Novel Mutations across Tumor Spectra.
Chmielecki J et al.·Cancer Res
2017
Glutamate triggers intracellular Ca(2+) oscillations and nitric oxide release by inducing NAADP- and InsP(3) -dependent Ca(2+) release in mouse brain endothelial cells.
Zuccolo E et al.·J Cell Physiol
2019Functional
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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