Seroatlas · Human Serome Atlas

SYNDIG1

Synapse differentiation-inducing gene protein 1

Also known as: C20orf39, DSPC2, FLJ14220, IFITMD5, SYNG1_HUMAN, TMEM90B

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

Protein identityUniProt · HPA

UniProt accession: Q9H7V2
Gene: SYNDIG1
Ensembl: ENSG00000101463
Chromosome: 20
Canonical length: 258 aa
Protein class: Predicted membrane proteins, Transporters
Subcellular location: Vesicles
Quaternary structure: Homodimer

OverviewNCBI Gene

This gene encodes a protein that belongs to the interferon-induced transmembrane family of proteins. A similar protein in rat is thought to regulate the development of excitatory synapses. [provided by RefSeq, Jul 2013]

Canonical amino-acid sequenceUniProt

258 residues, UniProt reviewed canonical sequence.

>Q9H7V2|SYNDIG1
     1  MDGIIEQKSM LVHSKISDAG KRNGLINTRN LMAESRDGLV SVYPAPQYQS HRVGASTVPA
    61  SLDSSRSEPM QQLLDPNTLQ QSVESRYRPN IILYSEGVLR SWGDGVAADC CETTFIEDRS
   121  PTKDSLEYPD GKFIDLSADD IKIHTLSYDV EEEEEFQELE SDYSSDTESE DNFLMMPPRD
   181  HLGLSVFSML CCFWPLGIAA FYLSHETNKA VAKGDLHQAS TSSRRALFLA VLSITIGTGV
   241  YVGVAVALIA YLSKNNHL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SYNDIG1 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: 1
Mean surface accessibility (rSASA): 0.65
Highest tissue expression: 45 nTPM

Expression across tissuesHPA

Tissue

spinal cord: 45 nTPM
cerebellum: 38 nTPM
cerebral cortex: 31 nTPM
heart muscle: 26 nTPM
hippocampal formation: 23 nTPM
midbrain: 22 nTPM

Single-cell type

microglia: 2,387 nCPM
oligodendrocytes: 279 nCPM
brain excitatory neurons: 144 nCPM
proximal tubule cells: 138 nCPM
cardiomyocytes: 136 nCPM
brain inhibitory neurons: 99 nCPM

Immune cell

basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM
MAIT T-cell: 0 nTPM

Brain region

white matter: 64 nTPM
pons: 51 nTPM
medulla oblongata: 50 nTPM
spinal cord: 50 nTPM
cerebellum: 48 nTPM
cerebral cortex: 46 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): 0.77
gnomAD pLI: 0.3
gnomAD missense Z: 0.51
DepMap mean gene effect: 0.21
DepMap dependency class: none

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

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of SYNDIG1 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 SYNDIG1 as an antibody target. Whether an autoantibody or antibody against SYNDIG1 could matter depends on whether native SYNDIG1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SYNDIG1 is annotated at the cell surface, where native SYNDIG1 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 SYNDIG1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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