Seroatlas · Human Serome Atlas

SDCBP

Syntenin-1

Also known as: MDA-9, SDCB1_HUMAN, SYCL

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

Protein identityUniProt · HPA

UniProt accession
O00560
Gene
SDCBP
Ensembl
ENSG00000137575
Chromosome
8
Canonical length
298 aa
Protein class
Plasma proteins, Predicted intracellular proteins, Transporters
Subcellular location
Nucleoplasm,Nuclear membrane,Cytosol
Secretome location
Intracellular and membrane
Quaternary structure
Homodimer

OverviewNCBI Gene

The protein encoded by this gene was initially identified as a molecule linking syndecan-mediated signaling to the cytoskeleton. The syntenin protein contains tandemly repeated PDZ domains that bind the cytoplasmic, C-terminal domains of a variety of transmembrane proteins. This protein may also affect cytoskeletal-membrane organization, cell adhesion, protein trafficking, and the activation of transcription factors. The protein is primarily localized to membrane-associated adherens junctions and focal adhesions but is also found at the endoplasmic reticulum and nucleus. Alternative splicing results in multiple transcript variants encoding different isoforms. Related pseudogenes have been identified on multiple chromosomes. [provided by RefSeq, Jan 2017]

Canonical amino-acid sequenceUniProt

298 residues, UniProt reviewed canonical sequence.

>O00560|SDCBP
     1  MSLYPSLEDL KVDKVIQAQT AFSANPANPA ILSEASAPIP HDGNLYPRLY PELSQYMGLS
    61  LNEEEIRANV AVVSGAPLQG QLVARPSSIN YMVAPVTGND VGIRRAEIKQ GIREVILCKD
   121  QDGKIGLRLK SIDNGIFVQL VQANSPASLV GLRFGDQVLQ INGENCAGWS SDKAHKVLKQ
   181  AFGEKITMTI RDRPFERTIT MHKDSTGHVG FIFKNGKITS IVKDSSAARN GLLTEHNICE
   241  INGQNVIGLK DSQIADILST SGTVVTITIM PAFIFEHIIK RMAPSIMKSL MDHTIPEV

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SDCBP 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
0
Mean surface accessibility (rSASA)
0.34
Highest tissue expression
248 nTPM

Expression across tissuesHPA

Tissue

  • placenta: 248 nTPM
  • urinary bladder: 232 nTPM
  • bone marrow: 232 nTPM
  • adipose tissue: 222 nTPM
  • lung: 211 nTPM
  • spleen: 191 nTPM

Single-cell type

  • neutrophils: 3,303 nCPM
  • melanocytes: 1,317 nCPM
  • extravillous trophoblasts: 1,137 nCPM
  • hofbauer cells: 1,105 nCPM
  • monocytes: 926 nCPM
  • mast cells: 732 nCPM

Immune cell

  • neutrophil: 1,916 nTPM
  • basophil: 779 nTPM
  • classical monocyte: 563 nTPM
  • eosinophil: 529 nTPM
  • total PBMC: 453 nTPM
  • intermediate monocyte: 350 nTPM

Brain region

  • white matter: 136 nTPM
  • medulla oblongata: 118 nTPM
  • pons: 114 nTPM
  • hypothalamus: 113 nTPM
  • thalamus: 113 nTPM
  • choroid plexus: 112 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SDCBP.

Disease | ImmuneIEDB

Conditions an epitope on SDCBP was assayed in.

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)
1.03
gnomAD pLI
0
gnomAD missense Z
1.04
DepMap mean gene effect
-0.07
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 7% 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 SDCBP 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 SDCBP as an antibody target. Whether an autoantibody or antibody against SDCBP could matter depends on whether native SDCBP is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SDCBP is annotated at the cell surface, where native SDCBP 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 SDCBP as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/SDCBP. 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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