Seroatlas · Human Serome Atlas

SYCP2

Synaptonemal complex protein 2

Also known as: SCP2, SYCP2_HUMAN

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

Protein identityUniProt · HPA

UniProt accession: Q9BX26
Gene: SYCP2
Ensembl: ENSG00000196074
Chromosome: 20
Canonical length: 1530 aa
Protein class: Disease related genes, Human disease related genes, Predicted intracellular proteins
Subcellular location: Nucleoplasm

OverviewNCBI Gene

The synaptonemal complex is a proteinaceous structure that links homologous chromosomes during the prophase of meiosis. The protein encoded by this gene is a major component of the synaptonemal complex and may bind DNA at scaffold attachment regions. The encoded protein requires synaptonemal complex protein 3, but not 1, for inclusion in the synaptonemal complex. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

1530 residues, UniProt reviewed canonical sequence.

>Q9BX26|SYCP2
     1  MPIRPDLQQL EKCIDDALRK NDFKPLKTLL QIDICEDVKI KCSKQFFHKV DNLICRELNK
    61  EDIHNVSAIL VSVGRCGKNI SVLGQAGLLT MIKQGLIQKM VAWFEKSKDI IQSQGNSKDE
   121  AVLNMIEDLV DLLLVIHDVS DEGKKQVVES FVPRICSLVI DSRVNICIQQ EIIKKMNAML
   181  DKMPQDARKI LSNQEMLILM SSMGERILDA GDYDLQVGIV EALCRMTTEK QRQELAHQWF
   241  SMDFIAKAFK RIKDSEFETD CRIFLNLVNG MLGDKRRVFT FPCLSAFLDK YELQIPSDEK
   301  LEEFWIDFNL GSQTLSFYIA GDNDDHQWEA VTVPEEKVQI YSIEVRESKK LLTIILKNTV
   361  KISKREGKEL LLYFDASLEI TNVTQKIFGA TKHRESIRKQ GISVAKTSLH ILFDASGSQI
   421  LVPESQISPV GEELVSLKEK SKSPKEFAKP SKYIKNSDKG NRNNSQLEKT TPSKRKMSEA
   481  SMIVSGADRY TMRSPVLFSN TSIPPRRRRI KPPLQMTSSA EKPSVSQTSE NRVDNAASLK
   541  SRSSEGRHRR DNIDKHIKTA KCVENTENKN VEFPNQNFSE LQDVIPDSQA AEKRDHTILP
   601  GVLDNICGNK IHSKWACWTP VTNIELCNNQ RASTSSGDTL NQDIVINKKL TKQKSSSSIS
   661  DHNSEGTGKV KYKKEQTDHI KIDKAEVEVC KKHNQQQNHP KYSGQKNTEN AKQSDWPVES
   721  ETTFKSVLLN KTIEESLIYR KKYILSKDVN TATCDKNPSA SKNVQSHRKA EKELTSELNS
   781  WDSKQKKMRE KSKGKEFTNV AESLISQINK RYKTKDDIKS TRKLKESLIN SGFSNKPVVQ
   841  LSKEKVQKKS YRKLKTTFVN VTSECPVNDV YNFNLNGADD PIIKLGIQEF QATAKEACAD
   901  RSIRLVGPRN HDELKSSVKT KDKKIITNHQ KKNLFSDTET EYRCDDSKTD ISWLREPKSK
   961  PQLIDYSRNK NVKNHKSGKS RSSLEKGQPS SKMTPSKNIT KKMDKTIPEG RIRLPRKATK
  1021  TKKNYKDLSN SESECEQEFS HSFKENIPVK EENIHSRMKT VKLPKKQQKV FCAETEKELS
  1081  KQWKNSSLLK DAIRDNCLDL SPRSLSGSPS SIEVTRCIEK ITEKDFTQDY DCITKSISPY
  1141  PKTSSLESLN SNSGVGGTIK SPKNNEKNFL CASESCSPIP RPLFLPRHTP TKSNTIVNRK
  1201  KISSLVLTQE TQNSNSYSDV SSYSSEERFM EIESPHINEN YIQSKREESH LASSLSKSSE
  1261  GREKTWFDMP CDATHVSGPT QHLSRKRIYI EDNLSNSNEV EMEEKGERRA NLLPKKLCKI
  1321  EDADHHIHKM SESVSSLSTN DFSIPWETWQ NEFAGIEMTY ETYERLNSEF KRRNNIRHKM
  1381  LSYFTTQSWK TAQQHLRTMN HQSQDSRIKK LDKFQFIIIE ELENFEKDSQ SLKDLEKEFV
  1441  DFWEKIFQKF SAYQKSEQQR LHLLKTSLAK SVFCNTDSEE TVFTSEMCLM KEDMKVLQDR
  1501  LLKDMLEEEL LNVRRELMSV FMSHERNANV

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against SYCP2 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: 40 nTPM

Expression across tissuesHPA

Tissue

testis: 40 nTPM
breast: 13 nTPM
pancreas: 6.2 nTPM
stomach: 5.8 nTPM
salivary gland: 4.2 nTPM
kidney: 4.1 nTPM

Single-cell type

early primary spermatocytes: 515 nCPM
late primary spermatocytes: 320 nCPM
oocytes: 143 nCPM
neutrophils: 89 nCPM
bergmann glia: 73 nCPM
differentiating spermatogonia: 51 nCPM

Immune cell

gdT-cell: 0.8 nTPM
MAIT T-cell: 0.8 nTPM
basophil: 0.7 nTPM
eosinophil: 0.7 nTPM
neutrophil: 0.7 nTPM
memory CD8 T-cell: 0.5 nTPM

Brain region

cerebellum: 27 nTPM
cerebral cortex: 17 nTPM
white matter: 15 nTPM
basal ganglia: 13 nTPM
thalamus: 12 nTPM
amygdala: 11 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about SYCP2.

Disease | AllUniProt

Conditions SYCP2 is implicated in, by any mechanism.

Spermatogenic failure 1 (SPGF1) MIM:258150

Disease | GeneticClinVar

6 pathogenic / likely-pathogenic of 238 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Oligosynaptic infertility
Non-obstructive azoospermia
Cryptozoospermia
Spermatocyte maturation arrest
Male infertility with azoospermia or oligozoospermia due to single gene mutation

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): 0.18
gnomAD pLI: 1
gnomAD missense Z: 0.26
DepMap mean gene effect: 0.04
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% 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 SYCP2 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 SYCP2 as an antibody target. Whether an autoantibody or antibody against SYCP2 could matter depends on whether native SYCP2 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

SYCP2 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 SYCP2 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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