Seroatlas · Human Serome Atlas

BEND3

BEN domain-containing protein 3

Also known as: BEND3_HUMAN, KIAA1553

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q5T5X7
Gene: BEND3
Ensembl: ENSG00000178409
Chromosome: 6
Canonical length: 828 aa
Protein class: Predicted intracellular proteins
Subcellular location: Nucleoplasm
Quaternary structure: Homooctamer

OverviewNCBI Gene

Enables rDNA binding activity. Involved in negative regulation of macromolecule biosynthetic process; positive regulation of ATP metabolic process; and protein homooligomerization. Located in heterochromatin; nucleolus; and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

Canonical amino-acid sequenceUniProt

828 residues, UniProt reviewed canonical sequence.

>Q5T5X7|BEND3
     1  MNSTEFTEDV EEVLKSITVK VETEAEDAAL DCSVNSRTSE KHSVDSVLTA LQDSSKRKQL
    61  VSDGLLDSVP GVKRRRLIPE ALLAGMRNRE NSSPCQGNGE QAGRGRSLGN VWPGEEEPCN
   121  DATTPSYKKP LYGISHKIME KKNPPSGDLL NVYELFEKAN ASNSPSSLRL LNEPQKRDCG
   181  STGAGTDNDP NIYFLIQKMF YMLNTLTSNM SQLHSKVDLL SLEVSRIKKQ VSPTEMVAKF
   241  QPPPEYQLTA AELKQIVDQS LSGGDLACRL LVQLFPELFS DVDFSRGCSA CGFAAKRKLE
   301  SLHLQLIRNY VEVYYPSVKD TAVWQAECLP QLNDFFSRFW AQREMEDSQP SGQVASFFEA
   361  EQVDPGHFLD NKDQEEALSL DRSSTIASDH VVDTQDLTEF LDEASSPGEF AVFLLHRLFP
   421  ELFDHRKLGE QYSCYGDGGK QELDPQRLQI IRNYTEIYFP DMQEEEAWLQ QCAQRINDEL
   481  EGLGLDAGSE GDPPRDDCYD SSSLPDDISV VKVEDSFEGE RPGRRSKKIW LVPIDFDKLE
   541  IPQPDFEVPG ADCLLSKEQL RSIYESSLSI GNFASRLLVH LFPELFTHEN LRKQYNCSGS
   601  LGKKQLDPSR IKLIRHYVQL LYPRAKNDRV WTLEFVGKLD ERCRRRDTEQ RRSYQQQRKV
   661  HVPGPECRDL TSYAINPERF REEFEGPPLP PERSSKDFCK IPLDELVVPS PDFPVPSPYL
   721  LSDKEVREIV QQSLSVGNFA ARLLVRLFPE LFTAENLRLQ YNHSGACNKK QLDPTRLRLI
   781  RHYVEAVYPV EKMEEVWHYE CIPSIDERCR RPNRKKCDIL KKAKKVEK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against BEND3 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.47
Highest tissue expression: 1.9 nTPM

Expression across tissuesHPA

Tissue

stomach: 1.9 nTPM
testis: 1.7 nTPM
colon: 1.4 nTPM
pancreas: 1.4 nTPM
rectum: 1.4 nTPM
salivary gland: 1.4 nTPM

Single-cell type

respiratory deuterosomal cells: 14 nCPM
respiratory ionocytes: 13 nCPM
podocytes: 10 nCPM
late spermatids: 9.4 nCPM
undifferentiated spermatogonia: 8.5 nCPM
choroid plexus epithelial cells: 8.2 nCPM

Immune cell

eosinophil: 0.1 nTPM
memory B-cell: 0.1 nTPM
basophil: 0 nTPM
classical monocyte: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM

Brain region

cerebellum: 6.2 nTPM
thalamus: 4.1 nTPM
amygdala: 4 nTPM
white matter: 3.8 nTPM
cerebral cortex: 3.6 nTPM
spinal cord: 3.5 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.35
gnomAD pLI: 0.94
gnomAD missense Z: 2.31
DepMap mean gene effect: -0.03
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

DNA methylation-dependent constitutive heterochromatin formation
negative regulation of transcription by RNA polymerase II
protein homooligomerization
rDNA heterochromatin formation
positive regulation of ATP metabolic process

Molecular functions

rDNA binding

Cellular components

Protein domainsUniProt · Pfam · InterPro

BEN domain
BEN domain
BEN domain-containing protein 3

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of BEND3 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads BEND3 as an antibody target. Whether an autoantibody or antibody against BEND3 could matter depends on whether native BEND3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

BEND3 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label BEND3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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