BEND3

Chr 6

BEN domain containing 3

Also known as: KIAA1553

NCBI Gene: 57673 ENSG00000178409 UniProt: Q5T5X7 OMIM: 616374

BEND3 encodes a transcriptional repressor that associates with the nucleolar remodeling complex to repress ribosomal DNA transcription and recruits the Polycomb repressive complex 2 to heterochromatin. Mutations cause autosomal dominant intellectual disability with microcephaly and seizures, typically presenting in infancy or early childhood. This gene is highly constrained against loss-of-function variants, indicating that such mutations are likely to be pathogenic.

OMIM ResearchSummary from RefSeq, UniProt

Enables rDNA binding activity. Involved in several processes, including heterochromatin formation; positive regulation of ATP metabolic process; and protein homooligomerization. Located in heterochromatin and nucleolus. [provided by Alliance of Genome Resources, Jun 2026]

OMIM ResearchGenerating clinical summary…

Clinical highlights

Interpreting a novel variant

This gene is strongly intolerant of loss-of-function variation in the population, so LoF variants warrant close attention. No curated mechanism annotation is available — see the mechanism card for the computational prediction and its caveats.Based on population constraint only.

Active trials

—

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

0.35

LOEUF· LoF intol.

LOF

Mechanism· predicted