U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

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

Gene ID: 10388, updated on 14-Nov-2024

Summary

Go to the top of the page Help
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
NEW
Try the new Gene table
Try the new Transcript table

Genomic context

Go to the top of the page Help
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

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. 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

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
Oligosynaptic infertility
MedGen: C0403810 OMIM: 258150 GeneReviews: Not available
Compare labs

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

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 female meiotic nuclear division 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 male meiotic nuclear division IEA
Inferred from Electronic Annotation
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 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

Go to the top of the page Help
Preferred Names
synaptonemal complex protein 2
Names
synaptonemal complex lateral element protein

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_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.

Chemical Information
Molecular Biology Databases
Research Materials
Tools
Miscellaneous