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10 sources retrieved · Most recent: April 2026 · Index updated 14 days ago
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SPCS3
signal peptidase complex subunit 3
Chromosome 4 · 4q34.2
NCBI Gene: 60559Ensembl: ENSG00000129128.13HGNC: HGNC:26212UniProt: P61009
76PubMed Papers
20Diseases
0Drugs
0Pathogenic Variants
DATA QUALITY
✓ Experimental GO Evidence✓ Swiss-Prot Reviewed
protein bindingproteolysisprotein processingviral protein processingneurodegenerative diseasedengue diseasebrain aneurysmAbnormality of the skeletal system
✦AI Summary

SPCS3 (signal peptidase complex subunit 3) is a catalytic subunit of the signal peptidase complex (SPC), an essential endoplasmic reticulum membrane enzyme that cleaves signal peptides from secretory pre-proteins with specificity determined by hydrophobic segment length 1. The human SPC exists in two functional paralogs with distinct proteolytic activities, featuring a catalytic triad at an active site that abuts the ER membrane, creating a transmembrane window that locally thins the lipid bilayer 1. SPCS3 plays critical roles in viral infection. It functions as a host restriction factor against chikungunya virus (CHIKV), binding the E1 glycoprotein with antiviral activity; CHIKV undergoes positive selection to overcome this restriction, with E1 residue V220 being essential for counteracting SPCS3-mediated inhibition 23. SPCS3 also participates in normal adipogenesis through retrotransposed paralog genes (Arxes1/2) that evolved tissue-specific functions distinct from the parental gene 4. Clinically, SPCS3 defects contribute to isolated growth hormone deficiency when minor spliceosome mutations impair U12-type intron splicing of the SPCS3 gene, causing pituitary hypoplasia 5. While SPC catalytic subunit SEC11A serves as a prognostic biomarker in head and neck squamous cell carcinoma 6, SPCS3 itself shows expression variation with potential eQTN associations in schizophrenia and bipolar disorder 7.

Sources cited
1
SPCS3 is a catalytic subunit of the signal peptidase complex; SPC removes signal peptides from secretory pre-proteins with specificity based on hydrophobic segment length; atomic structure reveals catalytic triad and transmembrane window
PMID: 34388369
2
SPCS3 is an E1-binding host restriction factor against CHIKV with antiviral activity; CHIKV E1 residue V220 is essential for counteracting SPCS3 and eIF3k interaction
PMID: 39261662
3
SPCS3 is an E1-binding protein with inhibitory activity against CHIKV production; CHIKV glycoproteins have been evolutionarily selected to counteract SPCS3
PMID: 37398144
4
SPCS3 gave rise to retrotransposed paralog genes (Arxes1/2) that function in adipogenesis; SPCS3 itself is dispensable for adipogenesis, indicating functional divergence
PMID: 21177646
5
SPCS3 is among defective transcripts resulting from minor spliceosome mutations causing isolated familial growth hormone deficiency and pituitary hypoplasia
PMID: 24480542
6
SPCS3 gene at chromosome 4q34 contains significant eQTNs in schizophrenia and bipolar disorder linkage analysis
PMID: 31695175
Disease Associationsⓘ20
neurodegenerative diseaseOpen Targets
0.53Moderate
dengue diseaseOpen Targets
0.46Moderate
brain aneurysmOpen Targets
0.21Weak
Abnormality of the skeletal systemOpen Targets
0.21Weak
gastritisOpen Targets
0.18Weak
cervical disc degenerative disorderOpen Targets
0.15Weak
ovarian neoplasmOpen Targets
0.13Weak
major depressive disorderOpen Targets
0.13Weak
pneumococcal pneumoniaOpen Targets
0.13Weak
glaucomaOpen Targets
0.12Weak
breast carcinomaOpen Targets
0.11Weak
edemaOpen Targets
0.08Suggestive
preeclampsiaOpen Targets
0.04Suggestive
hyperlipidemiaOpen Targets
0.03Suggestive
liver diseaseOpen Targets
0.03Suggestive
metabolic diseaseOpen Targets
0.03Suggestive
chronic laryngitisOpen Targets
0.03Suggestive
alcohol drinkingOpen Targets
0.03Suggestive
schizophreniaOpen Targets
0.03Suggestive
hypothyroidismOpen Targets
0.03Suggestive
Pathogenic Variants
No pathogenic variants reported on ClinVar for this gene.
View on ClinVar ↗
Related Genes
SEC11AProtein interaction77%SPCS1Protein interaction76%SSR1Protein interaction73%SSR3Protein interaction73%SEC11CProtein interaction62%SPCS2Protein interaction56%
Tissue Expression6 tissues
Bone Marrow
100%
Heart
59%
Lung
53%
Liver
47%
Brain
39%
Ovary
26%
Gene Interaction Network
Click a node to explore
SPCS3SEC11ASPCS1SSR1SSR3SEC11CSPCS2
PROTEIN STRUCTURE
Preparing viewer…
PDB7P2P · 4.90 Å · EM
View on RCSB ↗
Constraintⓘ
LOEUFⓘ
0.62LoF Tolerant
pLIⓘ
0.84Intermediate
Observed/Expected LoF0.00 [0.00–0.62]
RankingsWhere SPCS3 stands among ~20K protein-coding genes
  • #6,289of 20,598
    Most Researched76
  • #4,371of 17,882
    Most Constrained (LOEUF)0.62 · top quartile
Genes detectedSPCS3
Sources retrieved10 papers
Response time—
📄 Sources
10▼
1
Interaction of chikungunya virus glycoproteins with macrophage factors controls virion production.
PMID: 39261662
EMBO J · 2024
1.00
2
Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage.
PMID: 34388369
Mol Cell · 2021
0.90
3
Arxes: retrotransposed genes required for adipogenesis.
PMID: 21177646
Nucleic Acids Res · 2011
0.80
4
Chikungunya virus glycoproteins transform macrophages into productive viral dissemination vessels.
PMID: 37398144
bioRxiv · 2023
0.70
5
Defective minor spliceosome mRNA processing results in isolated familial growth hormone deficiency.
PMID: 24480542
EMBO Mol Med · 2014
0.60