Seroatlas · Human Serome Atlas

SDC4

Syndecan-4

Also known as: amphiglycan, ryudocan, SDC4_HUMAN, SYND4

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

Protein identityUniProt · HPA

UniProt accession: P31431
Gene: SDC4
Ensembl: ENSG00000124145
Chromosome: 20
Canonical length: 198 aa
Protein class: Cancer-related genes, Predicted membrane proteins, Predicted secreted proteins, Transporters
Subcellular location: Golgi apparatus,Plasma membrane
Secretome location: Secreted to blood
Quaternary structure: Homodimer

OverviewNCBI Gene

The protein encoded by this gene is a transmembrane (type I) heparan sulfate proteoglycan that functions as a receptor in intracellular signaling. The encoded protein is found as a homodimer and is a member of the syndecan proteoglycan family. This gene is found on chromosome 20, while a pseudogene has been found on chromosome 22. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

198 residues, UniProt reviewed canonical sequence.

>P31431|SDC4
     1  MAPARLFALL LFFVGGVAES IRETEVIDPQ DLLEGRYFSG ALPDDEDVVG PGQESDDFEL
    61  SGSGDLDDLE DSMIGPEVVH PLVPLDNHIP ERAGSGSQVP TEPKKLEENE VIPKRISPVE
   121  ESEDVSNKVS MSSTVQGSNI FERTEVLAAL IVGGIVGILF AVFLILLLMY RMKKKDEGSY
   181  DLGKKPIYKK APTNEFYA

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SDC4 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: Secreted
Secreted: Yes
Transmembrane segments: 1
Mean surface accessibility (rSASA): 0.66
Highest tissue expression: 384 nTPM

Expression across tissuesHPA

Tissue

liver: 384 nTPM
choroid plexus: 188 nTPM
skin: 181 nTPM
lung: 159 nTPM
kidney: 150 nTPM
stomach: 132 nTPM

Single-cell type

alveolar cells type 2: 878 nCPM
transitional alveolar cells: 573 nCPM
epididymal efferent duct ciliated cells: 541 nCPM
epididymal efferent duct absorptive cells: 433 nCPM
salivary duct cells: 412 nCPM
ocular epithelial cells: 399 nCPM

Immune cell

T-reg: 4.4 nTPM
MAIT T-cell: 2 nTPM
memory CD4 T-cell: 2 nTPM
classical monocyte: 1.6 nTPM
basophil: 1.5 nTPM
myeloid DC: 1.5 nTPM

Brain region

thalamus: 259 nTPM
midbrain: 200 nTPM
medulla oblongata: 189 nTPM
basal ganglia: 176 nTPM
pons: 134 nTPM
spinal cord: 123 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): 1.13
gnomAD pLI: 0
gnomAD missense Z: -0.12
DepMap mean gene effect: 0
DepMap dependency class: none

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 SDC4 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 SDC4 as an antibody target. Whether an autoantibody or antibody against SDC4 could matter depends on whether native SDC4 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SDC4 is annotated as secreted, so native SDC4 circulates and is directly accessible to antibodies. Secreted and cell-surface proteins are the autoantibody targets most likely to act like drugs, blocking or depleting the native protein.

Annotation status

The present source text does not explicitly label SDC4 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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