BEND3

protein-coding

BEN domain containing 3, the group of BEN domain containing

Gene summary

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]

Previous symbols:

KIAA1553

MANE transcript

NM_001367314.1

Inheritance

—

ClinVar variants

U:104B:7

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr6:107,065,182-107,115,515

External References & Databases

Ensembl (ENSG00000178409)

Transcript & Mutation Effects

hg38 • Region Span ~50.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BEND3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 108

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001367314.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar	1 clinvar	2
missense			102 clinvar	5 clinvar		107
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	104	6	1	111

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 36 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001367314.1	RefSeq	NP_001354243.1	3	MANE Select
ENST00000369042.6	Ensembl	ENSP00000358038.1	3	MANE Select
NM_001080450.3	RefSeq	NP_001073919.1	3	Standard
ENST00000429433.3	Ensembl	ENSP00000411268.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

negative regulation of transcription by RNA polymerase II
chromatin silencing at rDNA
DNA methylation
histone H4-K20 trimethylation
histone H3-K9 trimethylation

Molecular Function

rDNA binding
protein binding

Cellular Component

nucleoplasm
nuclear heterochromatin
nucleolus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000429433
Coding exons: 3
Length: 50088
Individuals with no LoFs: 125739
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125748
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.31	404	558	0.724	0.0000394	5443
Missense (PolyPhen)		155	263.53	0.58817		2370
Synonymous	-1.12	281	258	1.09	0.0000195	1666
Loss of Function	4.03	4	26.3	0.152	0.00000123	293

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.000018	0.000018	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Transcriptional repressor which associates with the NoRC (nucleolar remodeling complex) complex and plays a key role in repressing rDNA transcription. The sumoylated form modulates the stability of the NoRC complex component BAZ2A/TIP5 by controlling its USP21-mediated deubiquitination (PubMed:21914818, PubMed:26100909). Binds to unmethylated major satellite DNA and is involved in the recruitment of the Polycomb repressive complex 2 (PRC2) to major satellites (By similarity). Stimulates the ERCC6L translocase and ATPase activities (PubMed:28977671). {ECO:0000250|UniProtKB:Q6PAL0, ECO:0000269|PubMed:21914818, ECO:0000269|PubMed:26100909, ECO:0000269|PubMed:28977671}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.0480
RVIS EVS: -1.06
RVIS percentile EVS: 7.54

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.895

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium