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    SYCP2 synaptonemal complex protein 2 [ Homo sapiens (human) ]

    Gene ID: 10388, updated on 28-Oct-2024

    Summary

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    Official Symbol
    SYCP2provided by HGNC
    Official Full Name
    synaptonemal complex protein 2provided by HGNC
    Primary source
    HGNC:HGNC:11490
    See related
    Ensembl:ENSG00000196074 MIM:604105; AllianceGenome:HGNC:11490
    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
    SCP2; SCP-2; SPGF1
    Summary
    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]
    Expression
    Biased expression in testis (RPKM 17.7), stomach (RPKM 1.7) and 4 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SYCP2 in Genome Data Viewer
    Location:
    20q13.33
    Exon count:
    45
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (59863571..59933637, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (61647855..61717909, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (58438626..58508692, complement)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene phosphatase and actin regulator 3 Neighboring gene PHACTR3 antisense RNA 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18189 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18190 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr20:58325659-58326160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 18191 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr20:58345121-58346320 Neighboring gene RNA, U7 small nuclear 141 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13090 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 13091 Neighboring gene Sharpr-MPRA regulatory region 25 Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:58529519-58530020 Neighboring gene family with sequence similarity 217 member B Neighboring gene protein phosphatase 1 regulatory subunit 3D Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr20:58569287-58569819 Neighboring gene cadherin 26

    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 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. Novel Loss-of-Function SYCP2 Variants in Infertile Males Upgrade the Gene-Disease Clinical Validity Classification for SYCP2 and Male Infertility to Strong. Li J, et al. Genes (Basel), 2024 Aug 19. PMID 39202451, Free PMC Article
    2. Deregulation of SYCP2 predicts early stage human papillomavirus-positive oropharyngeal carcinoma: A prospective whole transcriptome analysis. Masterson L, et al. Cancer Sci, 2015 Nov. PMID 26334652, Free PMC Article
    3. SCP2: a major protein component of the axial elements of synaptonemal complexes of the rat. Offenberg HH, et al. Nucleic Acids Res, 1998 Jun 1. PMID 9592139, Free PMC Article
    4. SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility. Schilit SLP, et al. Am J Hum Genet, 2020 Jan 2. PMID 31866047, Free PMC Article
    5. Isolation and characterization of the human SCP2 cDNA and chromosomal localization of the gene. Schalk JA, et al. Mamm Genome, 1999 Jun. PMID 10341103

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Novel Loss-of-Function SYCP2 Variants in Infertile Males Upgrade the Gene-Disease Clinical Validity Classification for SYCP2 and Male Infertility to Strong.
      Title: Novel Loss-of-Function SYCP2 Variants in Infertile Males Upgrade the Gene-Disease Clinical Validity Classification for SYCP2 and Male Infertility to Strong.
    2. SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility.
      Title: SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility.
    3. SYCP2 may contribute to genetic instability during HPV-associated cancer development
      Title: Deregulation of SYCP2 predicts early stage human papillomavirus-positive oropharyngeal carcinoma: A prospective whole transcriptome analysis.
    4. Observational study of gene-disease association. (HuGE Navigator)
      Title: Evaluation of 172 candidate polymorphisms for association with oligozoospermia or azoospermia in a large cohort of men of European descent.
    Submit: New GeneRIF Correction

    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
    Oligosynaptic infertility
    MedGen: C0403810 OMIM: 258150 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)

    Genotypes

    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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in ectopic germ cell programmed cell death IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in fertilization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in male genitalia morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in meiotic recombination checkpoint signaling IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of apoptotic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of developmental process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in negative regulation of reproductive process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in synaptonemal complex assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synaptonemal complex assembly NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in condensed chromosome, centromeric region IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in lateral element IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in lateral element ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in synaptonemal complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    synaptonemal complex protein 2
    Names
    synaptonemal complex lateral element protein

    NCBI Reference Sequences (RefSeq)

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    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_046980.1 RefSeqGene

      Range
      5045..75111
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_014258.4 → NP_055073.2  synaptonemal complex protein 2

      See identical proteins and their annotated locations for NP_055073.2

      Status: REVIEWED

      Source sequence(s)
      AL109928, AL158092, BX649108, DB636651
      Consensus CDS
      CCDS13482.1
      UniProtKB/Swiss-Prot
      A2RUE5, O75763, Q5JX11, Q9BX26, Q9NTX8, Q9UG27
      Related
      ENSP00000350162.2, ENST00000357552.8

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      59863571..59933637 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011528490.4 → XP_011526792.1  synaptonemal complex protein 2 isoform X4

    2. XM_017027587.2 → XP_016883076.1  synaptonemal complex protein 2 isoform X2

    3. XM_047439828.1 → XP_047295784.1  synaptonemal complex protein 2 isoform X7

    4. XM_047439827.1 → XP_047295783.1  synaptonemal complex protein 2 isoform X6

    5. XM_047439826.1 → XP_047295782.1  synaptonemal complex protein 2 isoform X5

    6. XM_011528487.4 → XP_011526789.1  synaptonemal complex protein 2 isoform X1

      See identical proteins and their annotated locations for XP_011526789.1

      Conserved Domains (2) summary
      pfam18581
      Location:17 → 191
      SYCP2_ARLD; Synaptonemal complex 2 armadillo-repeat-like domain
      pfam18584
      Location:285 → 396
      SYCP2_SLD; Synaptonemal complex 2 Spt16M-like domain

    7. XM_011528489.3 → XP_011526791.1  synaptonemal complex protein 2 isoform X3

      See identical proteins and their annotated locations for XP_011526791.1

      UniProtKB/Swiss-Prot
      A2RUE5, O75763, Q5JX11, Q9BX26, Q9NTX8, Q9UG27

    8. XM_011528488.3 → XP_011526790.1  synaptonemal complex protein 2 isoform X1

      See identical proteins and their annotated locations for XP_011526790.1

      Conserved Domains (2) summary
      pfam18581
      Location:17 → 191
      SYCP2_ARLD; Synaptonemal complex 2 armadillo-repeat-like domain
      pfam18584
      Location:285 → 396
      SYCP2_SLD; Synaptonemal complex 2 Spt16M-like domain

    9. XM_047439825.1 → XP_047295781.1  synaptonemal complex protein 2 isoform X3

      UniProtKB/Swiss-Prot
      A2RUE5, O75763, Q5JX11, Q9BX26, Q9NTX8, Q9UG27
      Related
      ENSP00000360040.2, ENST00000371001.6

    10. XM_017027586.2 → XP_016883075.1  synaptonemal complex protein 2 isoform X1

      Conserved Domains (2) summary
      pfam18581
      Location:17 → 191
      SYCP2_ARLD; Synaptonemal complex 2 armadillo-repeat-like domain
      pfam18584
      Location:285 → 396
      SYCP2_SLD; Synaptonemal complex 2 Spt16M-like domain

    11. XM_047439829.1 → XP_047295785.1  synaptonemal complex protein 2 isoform X8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      61647855..61717909 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054322836.1 → XP_054178811.1  synaptonemal complex protein 2 isoform X4

    2. XM_054322833.1 → XP_054178808.1  synaptonemal complex protein 2 isoform X2

    3. XM_054322839.1 → XP_054178814.1  synaptonemal complex protein 2 isoform X7

    4. XM_054322838.1 → XP_054178813.1  synaptonemal complex protein 2 isoform X6

    5. XM_054322837.1 → XP_054178812.1  synaptonemal complex protein 2 isoform X5

    6. XM_054322830.1 → XP_054178805.1  synaptonemal complex protein 2 isoform X1

    7. XM_054322834.1 → XP_054178809.1  synaptonemal complex protein 2 isoform X3

      UniProtKB/Swiss-Prot
      A2RUE5, O75763, Q5JX11, Q9BX26, Q9NTX8, Q9UG27

    8. XM_054322835.1 → XP_054178810.1  synaptonemal complex protein 2 isoform X3

      UniProtKB/Swiss-Prot
      A2RUE5, O75763, Q5JX11, Q9BX26, Q9NTX8, Q9UG27

    9. XM_054322831.1 → XP_054178806.1  synaptonemal complex protein 2 isoform X1

    10. XM_054322832.1 → XP_054178807.1  synaptonemal complex protein 2 isoform X1

    11. XM_054322840.1 → XP_054178815.1  synaptonemal complex protein 2 isoform X8

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9BX26.2 GenPept UniProtKB/Swiss-Prot:Q9BX26

    Gene LinkOut

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

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