Seroatlas · Human Serome Atlas

CLSTN3

Calsyntenin-3

Also known as: CDHR14, CSTN3, CSTN3_HUMAN, KIAA0726

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

Protein identityUniProt · HPA

UniProt accession
Q9BQT9
Gene
CLSTN3
Ensembl
ENSG00000139182
Chromosome
12
Canonical length
956 aa
Protein class
Plasma proteins, Predicted intracellular proteins, Predicted membrane proteins

OverviewNCBI Gene

Enables cell-cell adhesion mediator activity and neurexin family protein binding activity. Involved in L-ascorbic acid metabolic process and regulation of synapse assembly. Predicted to be located in several cellular components, including Golgi membrane; dendrite; and postsynaptic density. Predicted to be part of protein-containing complex. Predicted to be active in several cellular components, including GABA-ergic synapse; lipid droplet; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2025]

Canonical amino-acid sequenceUniProt

956 residues, UniProt reviewed canonical sequence.

>Q9BQT9|CLSTN3
     1  MTLLLLPLLL ASLLASCSCN KANKHKPWIE AEYQGIVMEN DNTVLLNPPL FALDKDAPLR
    61  YAGEICGFRL HGSGVPFEAV ILDKATGEGL IRAKEPVDCE AQKEHTFTIQ AYDCGEGPDG
   121  ANTKKSHKAT VHVRVNDVNE FAPVFVERLY RAAVTEGKLY DRILRVEAID GDCSPQYSQI
   181  CYYEILTPNT PFLIDNDGNI ENTEKLQYSG ERLYKFTVTA YDCGKKRAAD DAEVEIQVKP
   241  TCKPSWQGWN KRIEYAPGAG SLALFPGIRL ETCDEPLWNI QATIELQTSH VAKGCDRDNY
   301  SERALRKLCG AATGEVDLLP MPGPNANWTA GLSVHYSQDS SLIYWFNGTQ AVQVPLGGPS
   361  GLGSGPQDSL SDHFTLSFWM KHGVTPNKGK KEEETIVCNT VQNEDGFSHY SLTVHGCRIA
   421  FLYWPLLESA RPVKFLWKLE QVCDDEWHHY ALNLEFPTVT LYTDGISFDP ALIHDNGLIH
   481  PPRREPALMI GACWTEEKNK EKEKGDNSTD TTQGDPLSIH HYFHGYLAGF SVRSGRLESR
   541  EVIECLYACR EGLDYRDFES LGKGMKVHVN PSQSLLTLEG DDVETFNHAL QHVAYMNTLR
   601  FATPGVRPLR LTTAVKCFSE ESCVSIPEVE GYVVVLQPDA PQILLSGTAH FARPAVDFEG
   661  TNGVPLFPDL QITCSISHQV EAKKDESWQG TVTDTRMSDE IVHNLDGCEI SLVGDDLDPE
   721  RESLLLDTTS LQQRGLELTN TSAYLTIAGV ESITVYEEIL RQARYRLRHG AALYTRKFRL
   781  SCSEMNGRYS SNEFIVEVNV LHSMNRVAHP SHVLSSQQFL HRGHQPPPEM AGHSLASSHR
   841  NSMIPSAATL IIVVCVGFLV LMVVLGLVRI HSLHRRVSGA GGPPGASSDP KDPDLFWDDS
   901  ALTIIVNPME SYQNRQSCVT GAVGGQQEDE DSSDSEVADS PSSDERRIIE TPPHRY

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CLSTN3 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
Cell surface
Secreted
No
Transmembrane segments
2
Mean surface accessibility (rSASA)
0.36
Highest tissue expression
137 nTPM

Expression across tissuesHPA

Tissue

  • cerebellum: 137 nTPM
  • cerebral cortex: 93 nTPM
  • hypothalamus: 83 nTPM
  • liver: 46 nTPM
  • pituitary gland: 43 nTPM
  • hippocampal formation: 42 nTPM

Single-cell type

  • brain excitatory neurons: 100 nCPM
  • brain inhibitory neurons: 96 nCPM
  • other brain neurons: 91 nCPM
  • proximal tubule cells: 38 nCPM
  • distal convoluted tubule cells: 20 nCPM
  • loop of henle epithelial cells: 19 nCPM

Immune cell

  • NK-cell: 6.9 nTPM
  • gdT-cell: 3.3 nTPM
  • memory CD8 T-cell: 2.9 nTPM
  • T-reg: 2 nTPM
  • MAIT T-cell: 1.9 nTPM
  • basophil: 1.5 nTPM

Brain region

  • cerebral cortex: 154 nTPM
  • hypothalamus: 139 nTPM
  • pons: 120 nTPM
  • thalamus: 113 nTPM
  • basal ganglia: 113 nTPM
  • cerebellum: 102 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)
0.32
gnomAD pLI
0.97
gnomAD missense Z
1.5
DepMap mean gene effect
-0.1
DepMap dependency class
none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of CLSTN3 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 CLSTN3 as an antibody target. Whether an autoantibody or antibody against CLSTN3 could matter depends on whether native CLSTN3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CLSTN3 is annotated at the cell surface, where native CLSTN3 is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label CLSTN3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/CLSTN3. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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