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

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

    Summary

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    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
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    Genomic context

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    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

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: 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

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    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

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    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

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    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

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    Preferred Names
    synaptonemal complex protein 3

    NCBI Reference Sequences (RefSeq)

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    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.

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