BEND5

Chr 1

BEN domain containing 5

Also known as: C1orf165

NCBI Gene: 79656ENSG00000162373UniProt: Q7L4P6

Predicted to enable DNA binding activity. Involved in negative regulation of DNA-templated transcription. Predicted to be located in Golgi apparatus. [provided by Alliance of Genome Resources, Jul 2025]

66
ClinVar variants
7
Pathogenic / LP
0.05
pLI score
0
Active trials
Clinical Summary— BEND5
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.31) despite low pLI — interpret in context.
📋
ClinVar Variants
7 Pathogenic / Likely Pathogenic· 56 VUS of 66 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.66LOEUF
pLI 0.054
Z-score 2.54
OE 0.31 (0.16–0.66)
Tolerant

Typical tolerance to LoF variation

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
1.70Z-score
OE missense 0.68 (0.59–0.78)
152 obs / 223.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.31 (0.16–0.66)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.68 (0.59–0.78)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.07
0≤1.21.6
LoF obs/exp: 5 / 16.0Missense obs/exp: 152 / 223.7Syn Z: -0.54

ClinVar Variant Classifications

66 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic4
Likely Pathogenic3
VUS56
Likely Benign3
4
Pathogenic
3
Likely Pathogenic
56
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
4
0
4
Likely Pathogenic
0
0
3
0
3
VUS
0
50
6
0
56
Likely Benign
0
0
0
3
3
Benign
0
0
0
0
0
Total05013366

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

View in 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.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Investigation of the function of the novel tumor marker BEND5 in lung adenocarcinoma based on data mining and in vitro analysis.
Ma Y et al.·J Thorac Dis
2023🔓 Open Access
Interaction between BEND5 and RBPJ suppresses breast cancer growth and metastasis via inhibiting Notch signaling.
Shi Y et al.·Int J Biol Sci
2022🔓 Open Access
Hypermethylation of BEND5 contributes to cell proliferation and is a prognostic marker of colorectal cancer.
Lin RK et al.·Oncotarget
2017🔓 Open Access
Comparison of immortalized bEnd5 and primary mouse brain microvascular endothelial cells as in vitro blood-brain barrier models for the study of T cell extravasation.
Steiner O et al.·J Cereb Blood Flow Metab
2011Functional
Evaluation of bEnd5 cell line as an in vitro model for the blood-brain barrier under normal and hypoxic/aglycemic conditions.
Yang T et al.·J Pharm Sci
2007Functional
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools