Seroatlas · Human Serome Atlas

SYCP3

Synaptonemal complex protein 3

Also known as: SYCP3_HUMAN

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

Protein identityUniProt · HPA

UniProt accession: Q8IZU3
Gene: SYCP3
Ensembl: ENSG00000139351
Chromosome: 12
Canonical length: 236 aa
Protein class: Disease related genes, Human disease related genes, Predicted intracellular proteins
Quaternary structure: Homotetramer

OverviewNCBI Gene

This gene encodes an essential structural component of the synaptonemal complex. This complex is involved in synapsis, recombination and segregation of meiotic chromosomes. Mutations in this gene are associated with azoospermia in males and susceptibility to pregnancy loss in females. Alternate splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, May 2010]

Canonical amino-acid sequenceUniProt

236 residues, UniProt reviewed canonical sequence.

>Q8IZU3|SYCP3
     1  MVSSGKKYSR KSGKPSVEDQ FTRAYDFETE DKKDLSGSEE DVIEGKTAVI EKRRKKRSSA
    61  GVVEDMGGEV QNMLEGVGVD INKALLAKRK RLEMYTKASL KTSNQKIEHV WKTQQDQRQK
   121  LNQEYSQQFL TLFQQWDLDM QKAEEQEEKI LNMFRQQQKI LQQSRIVQSQ RLKTIKQLYE
   181  QFIKSMEELE KNHDNLLTGA QNEFKKEMAM LQKKIMMETQ QQEIASVRKS LQSMLF

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SYCP3 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: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.55
Highest tissue expression: 78 nTPM

Expression across tissuesHPA

Tissue

testis: 78 nTPM
cerebellum: 0.7 nTPM
ovary: 0.5 nTPM
salivary gland: 0.5 nTPM
appendix: 0.3 nTPM
bone marrow: 0.2 nTPM

Single-cell type

early primary spermatocytes: 996 nCPM
cardiomyocytes: 667 nCPM
oocytes: 378 nCPM
late primary spermatocytes: 283 nCPM
differentiating spermatogonia: 193 nCPM
adipocytes: 67 nCPM

Immune cell

basophil: 0.6 nTPM
naive B-cell: 0.2 nTPM
classical monocyte: 0.1 nTPM
naive CD8 T-cell: 0.1 nTPM
neutrophil: 0.1 nTPM
eosinophil: 0 nTPM

Brain region

cerebellum: 3.3 nTPM
basal ganglia: 3 nTPM
cerebral cortex: 3 nTPM
amygdala: 2.6 nTPM
thalamus: 2.3 nTPM
hippocampal formation: 2.2 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SYCP3.

Disease | AllUniProt

Conditions SYCP3 is implicated in, by any mechanism.

Spermatogenic failure 4 (SPGF4) MIM:270960
Pregnancy loss, recurrent, 4 (RPRGL4) MIM:270960

Disease | GeneticClinVar

3 pathogenic / likely-pathogenic of 70 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

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): 0.95
gnomAD pLI: 0
gnomAD missense Z: 0.54
DepMap mean gene effect: 0.01
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

DNA binding

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of SYCP3 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 SYCP3 as an antibody target. Whether an autoantibody or antibody against SYCP3 could matter depends on whether native SYCP3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SYCP3 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label SYCP3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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