U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

SYCP3 synaptonemal complex protein 3 [ Homo sapiens (human) ]

Gene ID: 50511, updated on 2-Nov-2024

Summary

Go to the top of the page Help
Official Symbol
SYCP3provided by HGNC
Official Full Name
synaptonemal complex protein 3provided by HGNC
Primary source
HGNC:HGNC:18130
See related
Ensembl:ENSG00000139351 MIM:604759; AllianceGenome:HGNC:18130
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
COR1; SCP3; SPGF4; RPRGL4
Summary
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]
Expression
Broad expression in testis (RPKM 35.2), duodenum (RPKM 4.0) and 14 other tissues See more
Orthologs
mouse all
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
See SYCP3 in Genome Data Viewer
Location:
12q23.2
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (101728648..101739462, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (101689875..101700721, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (102122426..102133240, complement)

Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene myosin binding protein C1 Neighboring gene uncharacterized LOC124902996 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6864 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4769 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4770 Neighboring gene choline phosphotransferase 1 Neighboring gene RNY1 pseudogene 16 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6865 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 6866 Neighboring gene uncharacterized LOC124902997 Neighboring gene N-acetylglucosamine-1-phosphate transferase subunits alpha and beta Neighboring gene RNA, U6 small nuclear 101, pseudogene

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help
  • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

Go to the top of the pageHelp

Related articles in PubMed

  1. Kinetics of meiosis in azoospermic males: a joint histological and cytological approach. de Boer P, et al. Cytogenet Genome Res, 2004. PMID 15218256
  2. Testicular expression of synaptonemal complex protein 3 (SYCP3) messenger ribonucleic acid in 110 patients with nonobstructive azoospermia. Aarabi M, et al. Fertil Steril, 2006 Aug. PMID 16824523
  3. Synaptonemal complex protein 3 as a novel prognostic marker in early stage non-small cell lung cancer. Chung JY, et al. Hum Pathol, 2013 Apr. PMID 23069255, Free PMC Article
  4. Investigation of mutations in the synaptonemal complex protein 3 (SYCP3) gene among azoospermic infertile male patients in the Turkish population. Gurkan H, et al. Andrologia, 2013 Apr. PMID 22670862
  5. Synaptonemal complex protein 3 is a prognostic marker in cervical cancer. Cho H, et al. PLoS One, 2014. PMID 24905095, Free PMC Article

See all (41) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. SCP3 is associated with lymphangiogenesis and provides insight into the SCP3-VEGF-C/VEGF-D axis based cancer therapy strategy.
    Title: Synaptonemal complex protein 3 is associated with lymphangiogenesis in non-small cell lung cancer patients with lymph node metastasis.
  2. In the model, the reported compaction of chromosomal DNA caused by SYCP3 would result from its ability to bridge distant sites on a DNA molecule with the DNA-binding domains located at each end of its strut-like structure.
    Title: Single-molecule observation of DNA compaction by meiotic protein SYCP3.
  3. SYCP3 binds to RAD51 and attenuates RAD51 activity during meiosis.
    Title: SYCP3 regulates strand invasion activities of RAD51 and DMC1.
  4. SYCP3 binding and assembly on meiotic chromosomes leads to their organisation into compact structures compatible with recombination and crossover formation
    Title: A molecular model for the role of SYCP3 in meiotic chromosome organisation.
  5. The T657C polymorphism of the SYCP3 gene is possibly associated with recurrent pregnancy loss of unknown cause in human.
    Title: The T657C polymorphism on the SYCP3 gene is associated with recurrent pregnancy loss.
  6. SCP3 plays an important role in the progression of cervical cancer
    Title: Synaptonemal complex protein 3 is a prognostic marker in cervical cancer.
  7. SYCP3 mutations are not associated with the genetic susceptibility for meiotic arrest in infertile male patients with nonobstructive azoospermia in the Turkish population
    Title: Investigation of mutations in the synaptonemal complex protein 3 (SYCP3) gene among azoospermic infertile male patients in the Turkish population.
  8. screening for genetic variants in AURKB and SYCP3 among these patients with reproductive problems using Sanger sequencing. Only one apparently non-pathogenic deletion was found in SYCP3.
    Title: Mutation screening of AURKB and SYCP3 in patients with reproductive problems.
  9. Positive synaptonemal complex protein 3 expression is a portent of poor outcome and may be a potential biomarker in the early stages of the non-small cell lung cancer for survival.
    Title: Synaptonemal complex protein 3 as a novel prognostic marker in early stage non-small cell lung cancer.
  10. mutations in SYCP3 do not contribute significantly to risk for recurrent miscarriage through maternal meiotic nondisjunction.
    Title: Absence of SYCP3 mutations in women with recurrent miscarriage with at least one trisomic miscarriage.
Submit: New GeneRIF Correction See all GeneRIFs (21)

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Spermatogenic failure 4
MedGen: C0232981 OMIM: 270960 GeneReviews: Not available
Compare labs

Variation

Go to the top of the page Help

See Variation Viewer (GRCh37.p13)

Pathways from PubChem

Go to the top of the page

Interactions

Go to the top of the page Help
Products Interactant Other Gene Complex Source Pubs Description

General gene information

Go to the top of the page Help

Markers

Homology

Clone Names

  • MGC71888

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in cell division IEA
Inferred from Electronic Annotation
more info
  
involved_in male meiosis I NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in meiotic cell cycle IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in sperm DNA condensation IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in spermatid development IBA
Inferred from Biological aspect of Ancestor
more info
  
Component Evidence Code Pubs
located_in chromosome, centromeric region ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in lateral element ISS
Inferred from Sequence or Structural Similarity
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 
is_active_in synaptonemal complex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in synaptonemal complex IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

Go to the top of the page Help
Preferred Names
synaptonemal complex protein 3

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_021181.1 RefSeqGene

    Range
    5008..15822
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001177948.2 → NP_001171419.1  synaptonemal complex protein 3

    See identical proteins and their annotated locations for NP_001171419.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC063950, AF517774
    Consensus CDS
    CCDS9087.1
    UniProtKB/Swiss-Prot
    Q8IZU3
    Related
    ENSP00000266743.2, ENST00000266743.6
    Conserved Domains (1) summary
    pfam04803
    Location:83 → 214
    Cor1; Cor1/Xlr/Xmr conserved region

  2. NM_001177949.2 → NP_001171420.1  synaptonemal complex protein 3

    See identical proteins and their annotated locations for NP_001171420.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    AC063950, AF492003, BG201028
    Consensus CDS
    CCDS9087.1
    UniProtKB/Swiss-Prot
    Q8IZU3
    Related
    ENSP00000376655.1, ENST00000392924.2
    Conserved Domains (1) summary
    pfam04803
    Location:83 → 214
    Cor1; Cor1/Xlr/Xmr conserved region

  3. NM_153694.5 → NP_710161.1  synaptonemal complex protein 3

    See identical proteins and their annotated locations for NP_710161.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2 and 3 encode the same protein.
    Source sequence(s)
    BC062662, BG202454
    Consensus CDS
    CCDS9087.1
    UniProtKB/Swiss-Prot
    Q8IZU3
    Related
    ENSP00000376658.3, ENST00000392927.7
    Conserved Domains (1) summary
    pfam04803
    Location:83 → 214
    Cor1; Cor1/Xlr/Xmr conserved region

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000012.12 Reference GRCh38.p14 Primary Assembly

    Range
    101728648..101739462 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011538421.4 → XP_011536723.3  synaptonemal complex protein 3 isoform X1

  2. XM_005268927.3 → XP_005268984.1  synaptonemal complex protein 3 isoform X1

    See identical proteins and their annotated locations for XP_005268984.1

    Conserved Domains (1) summary
    pfam04803
    Location:83 → 214
    Cor1; Cor1/Xlr/Xmr conserved region

  3. XM_005268922.6 → XP_005268979.4  synaptonemal complex protein 3 isoform X1

  4. XM_005268924.2 → XP_005268981.1  synaptonemal complex protein 3 isoform X1

    See identical proteins and their annotated locations for XP_005268981.1

    Conserved Domains (1) summary
    pfam04803
    Location:83 → 214
    Cor1; Cor1/Xlr/Xmr conserved region

  5. XM_047428913.1 → XP_047284869.1  synaptonemal complex protein 3 isoform X1

  6. XM_005268926.5 → XP_005268983.1  synaptonemal complex protein 3 isoform X1

    See identical proteins and their annotated locations for XP_005268983.1

    Conserved Domains (1) summary
    pfam04803
    Location:83 → 214
    Cor1; Cor1/Xlr/Xmr conserved region

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060936.1 Alternate T2T-CHM13v2.0

    Range
    101689875..101700721 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054372144.1 → XP_054228119.1  synaptonemal complex protein 3 isoform X1

  2. XM_054372147.1 → XP_054228122.1  synaptonemal complex protein 3 isoform X1

  3. XM_054372143.1 → XP_054228118.1  synaptonemal complex protein 3 isoform X1

  4. XM_054372145.1 → XP_054228120.1  synaptonemal complex protein 3 isoform X1

  5. XM_054372146.1 → XP_054228121.1  synaptonemal complex protein 3 isoform X1

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8IZU3.1 GenPept UniProtKB/Swiss-Prot:Q8IZU3

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous