BEND5

Chr 1

BEN domain containing 5

Also known as: C1orf165

NCBI Gene: 79656 ENSG00000162373 UniProt: Q7L4P6 OMIM: 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.

OMIM ResearchSummary from RefSeq, UniProt

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]

OMIM ResearchGenerating clinical summary…

DNmechanismLOEUF 0.66

Clinical Summary— BEND5

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Population Constraint (gnomAD)

Constrained for loss-of-function variants (OE-LoF 0.31) despite low pLI — interpret in context.

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ClinVar Variants

50 VUS of 53 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?

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 OE?0.31 (0.16–0.66)

0≤0.351.4

Missense OE?0.68 (0.59–0.78)

0≤0.61.4

Synonymous OE?1.07

0≤1.21.6

LoF obs/exp: 5 / 16.0Missense obs/exp: 152 / 223.7Syn Z: -0.54

This gene — mechanism propensity

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

53 submitted variants in ClinVar

ClinVar

Classification Summary

VUS50

Likely Benign3

VUS

Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	Missense + Inframe	Synonymous	Total
Pathogenic	0	0	0
Likely Pathogenic	0	0	0
VUS	50	0	50
Likely Benign	0	3	3
Benign	0	0	0
Total	50	3	53

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

View in ClinVar →

7 pathogenic / likely-pathogenic (of 14) ClinVar copy-number / structural variants overlap BEND5 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →