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 R... See more...

Aliases for SYCP2 Gene

Aliases for SYCP2 Gene

  • Synaptonemal Complex Protein 2 2 3 4 5
  • SCP2 2 3 4
  • Synaptonemal Complex Lateral Element Protein 3 4
  • SCP-2 3 4
  • HsSCP2 4
  • SPGF1 3
  • SYCP2 5

External Ids for SYCP2 Gene

Previous GeneCards Identifiers for SYCP2 Gene

  • GC20M058167
  • GC20M059077
  • GC20M059124
  • GC20M057872
  • GC20M058438
  • GC20M055225

Summaries for SYCP2 Gene

Entrez Gene Summary for SYCP2 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]

GeneCards Summary for SYCP2 Gene

SYCP2 (Synaptonemal Complex Protein 2) is a Protein Coding gene. Diseases associated with SYCP2 include Spermatogenic Failure 1 and Tonsil Squamous Cell Carcinoma. Among its related pathways are Meiosis and Cell Cycle, Mitotic. Gene Ontology (GO) annotations related to this gene include protein heterodimerization activity. An important paralog of this gene is SYCP2L.

UniProtKB/Swiss-Prot Summary for SYCP2 Gene

  • Major component of the axial/lateral elements of synaptonemal complexes (SCS) during meiotic prophase. Plays a role in the assembly of synaptonemal complexes. Required for normal meiotic chromosome synapsis during oocyte and spermatocyte development and for normal male and female fertility. Required for insertion of SYCP3 into synaptonemal complexes. May be involved in the organization of chromatin by temporarily binding to DNA scaffold attachment regions. Requires SYCP3, but not SYCP1, in order to be incorporated into the axial/lateral elements.

Additional gene information for SYCP2 Gene

No data available for CIViC Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SYCP2 Gene

Genomics for SYCP2 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SYCP2 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH20J059933 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE CraniofacialAtlas 600.7 -0.2 -201 1.8 RNF2 SP1 CTCF ZBTB33 PRDM10 ZNF629 REST ZNF692 TARDBP ZHX2 FAM217B SYCP2 NELFCD PPP1R3D
GH20J059931 Enhancer 0.8 Ensembl ENCODE 600.7 +1.9 1877 1.4 ZBTB33 FOXA1 ZSCAN4 ZNF600 ZNF10 ZKSCAN1 ZNF8 ZBTB11 GATA3 NONO FAM217B SYCP2 lnc-PPP1R3D-5 PHACTR3
GH20J060054 Promoter/Enhancer 1.8 FANTOM5 Ensembl ENCODE CraniofacialAtlas dbSUPER 2 -123.3 -123289 4.8 CTCF ZBTB33 YBX1 PRDM10 ZNF629 KDM1A ZNF692 ZIC2 PATZ1 RAD21 C20orf197 PPP1R3D FAM217B SYCP2 LOC729296 CDH26 LOC105372698
GH20J059876 Enhancer 0.2 FANTOM5 7.8 +57.2 57151 0.4 FAM217B SYCP2 PPP1R3D lnc-PPP1R3D-8 RF00066-123 RNU7-141P PHACTR3
GH20J059861 Enhancer 0.3 FANTOM5 3.1 +72.1 72076 0.3 PKNOX1 PHACTR3 FAM217B SYCP2 RNU7-141P RF00066-123 lnc-PPP1R3D-8
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SYCP2 on the GeneHancer Hub at the UCSC Golden Path

Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for SYCP2

Top Transcription factor binding sites by QIAGEN in the SYCP2 gene promoter:
  • AhR
  • Arnt
  • E2F
  • E2F-1
  • ER-alpha
  • Olf-1
  • POU2F1
  • POU2F1a
  • USF-1:USF-2
  • USF2

Genomic Locations for SYCP2 Gene

Genomic Locations for SYCP2 Gene
chr20:59,863,277-59,933,700
(GRCh38/hg38)
Size:
70,424 bases
Orientation:
Minus strand
chr20:58,438,618-58,508,710
(GRCh37/hg19)
Size:
70,093 bases
Orientation:
Minus strand

Genomic View for SYCP2 Gene

Genes around SYCP2 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
SYCP2 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SYCP2 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SYCP2 Gene

Proteins for SYCP2 Gene

  • Protein details for SYCP2 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9BX26-SYCP2_HUMAN
    Recommended name:
    Synaptonemal complex protein 2
    Protein Accession:
    Q9BX26
    Secondary Accessions:
    • A2RUE5
    • O75763
    • Q5JX11
    • Q9NTX8
    • Q9UG27

    Protein attributes for SYCP2 Gene

    Size:
    1530 amino acids
    Molecular mass:
    175639 Da
    Quaternary structure:
    • Component of the lateral elements of synaptonemal complexes. Heterodimer with SYCP3 (By similarity). Interacts with SMC1A and SMC3 (By similarity). Interacts with TEX11 (By similarity).

neXtProt entry for SYCP2 Gene

Post-translational modifications for SYCP2 Gene

No data available for DME Specific Peptides for SYCP2 Gene

Domains & Families for SYCP2 Gene

Gene Families for SYCP2 Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for SYCP2 Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for SYCP2 Gene

GenScript: Design optimal peptide antigens:
  • Synaptonemal complex protein 2 (A2A340_HUMAN)
  • SYCP2 protein (A6QL60_HUMAN)
  • SYCP2 protein (Q8IWA1_HUMAN)
  • Synaptonemal complex lateral element protein (SYCP2_HUMAN)

Graphical View of Domain Structure for InterPro Entry

Q9BX26

UniProtKB/Swiss-Prot:

SYCP2_HUMAN :
  • Belongs to the SYCP2 family.
Family:
  • Belongs to the SYCP2 family.
genes like me logo Genes that share domains with SYCP2: view

Function for SYCP2 Gene

Molecular function for SYCP2 Gene

UniProtKB/Swiss-Prot Function:
Major component of the axial/lateral elements of synaptonemal complexes (SCS) during meiotic prophase. Plays a role in the assembly of synaptonemal complexes. Required for normal meiotic chromosome synapsis during oocyte and spermatocyte development and for normal male and female fertility. Required for insertion of SYCP3 into synaptonemal complexes. May be involved in the organization of chromatin by temporarily binding to DNA scaffold attachment regions. Requires SYCP3, but not SYCP1, in order to be incorporated into the axial/lateral elements.
GENATLAS Biochemistry:
synaptonemal complex protein 2,axial element homolog to mouse Scp2,DNA binding protein,involved in the structural organization of meiotic prophase chromosomes

Phenotypes From GWAS Catalog for SYCP2 Gene

Gene Ontology (GO) - Molecular Function for SYCP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003677 DNA binding NAS 10341103
genes like me logo Genes that share ontologies with SYCP2: view
genes like me logo Genes that share phenotypes with SYCP2: view

Human Phenotype Ontology for SYCP2 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for SYCP2 Gene

MGI Knock Outs for SYCP2:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYCP2

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for SYCP2 Gene

Localization for SYCP2 Gene

Subcellular locations from UniProtKB/Swiss-Prot for SYCP2 Gene

Nucleus. Chromosome. Note=In axial/lateral elements of the tripartite segments of synaptonemal complexes. {ECO:0000250 UniProtKB:Q9CUU3}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SYCP2 gene
Compartment Confidence
nucleus 5
extracellular 1
cytoskeleton 1
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Nucleoplasm (3)
  • Plasma membrane (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for SYCP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000780 condensed nuclear chromosome, centromeric region IBA 21873635
GO:0000795 synaptonemal complex NAS 10341103
GO:0000800 lateral element IBA,ISS --
GO:0005634 nucleus NAS 10341103
GO:0005694 chromosome IEA --
genes like me logo Genes that share ontologies with SYCP2: view

Pathways & Interactions for SYCP2 Gene

PathCards logo

SuperPathways for SYCP2 Gene

SuperPathway Contained pathways
1 Meiosis
.73
2 Cell Cycle, Mitotic
genes like me logo Genes that share pathways with SYCP2: view

Pathways by source for SYCP2 Gene

3 Reactome pathways for SYCP2 Gene

Gene Ontology (GO) - Biological Process for SYCP2 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000080 mitotic G1 phase IBA 21873635
GO:0007049 cell cycle IEA --
GO:0007130 synaptonemal complex assembly NAS 10341103
GO:0007140 male meiotic nuclear division IBA 21873635
GO:0007143 female meiotic nuclear division IBA 21873635
genes like me logo Genes that share ontologies with SYCP2: view

No data available for SIGNOR curated interactions for SYCP2 Gene

Drugs & Compounds for SYCP2 Gene

No Compound Related Data Available

Transcripts for SYCP2 Gene

mRNA/cDNA for SYCP2 Gene

1 REFSEQ mRNAs :
12 NCBI additional mRNA sequence :
9 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :

CRISPR Products

Inhibitory RNA Products

  • Search GeneCopoeia for shRNA, lentivirus and/or AAV clone products for SYCP2

Alternative Splicing Database (ASD) splice patterns (SP) for SYCP2 Gene

No ASD Table

Relevant External Links for SYCP2 Gene

GeneLoc Exon Structure for
SYCP2

Expression for SYCP2 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SYCP2 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for SYCP2 Gene

This gene is overexpressed in Testis (x10.4).

Protein differential expression in normal tissues from HIPED for SYCP2 Gene

This gene is overexpressed in Testis (24.9), Ovary (15.1), Platelet (12.5), and Heart (10.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for SYCP2 Gene



Protein tissue co-expression partners for SYCP2 Gene

- Elite partner

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SYCP2

SOURCE GeneReport for Unigene cluster for SYCP2 Gene:

Hs.202676

Evidence on tissue expression from TISSUES for SYCP2 Gene

  • Kidney(4.3)
genes like me logo Genes that share expression patterns with SYCP2: view

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for SYCP2 Gene

Orthologs for SYCP2 Gene

This gene was present in the common ancestor of chordates.

Orthologs for SYCP2 Gene

Organism Taxonomy Gene Similarity Type Details
Chimpanzee
(Pan troglodytes)
Mammalia SYCP2 30 31
  • 99.24 (n)
OneToOne
Dog
(Canis familiaris)
Mammalia SYCP2 30 31
  • 85.17 (n)
OneToOne
Cow
(Bos Taurus)
Mammalia SYCP2 30 31
  • 84.94 (n)
OneToOne
Mouse
(Mus musculus)
Mammalia Sycp2 30 17 31
  • 77.91 (n)
OneToOne
Rat
(Rattus norvegicus)
Mammalia Sycp2 30
  • 77.76 (n)
Platypus
(Ornithorhynchus anatinus)
Mammalia -- 31
  • 51 (a)
OneToMany
-- 31
  • 35 (a)
OneToMany
Oppossum
(Monodelphis domestica)
Mammalia SYCP2 31
  • 51 (a)
OneToOne
Chicken
(Gallus gallus)
Aves SYCP2 30 31
  • 58.15 (n)
OneToOne
Lizard
(Anolis carolinensis)
Reptilia SYCP2 31
  • 44 (a)
OneToOne
Tropical Clawed Frog
(Silurana tropicalis)
Amphibia sycp2 30
  • 54.54 (n)
Zebrafish
(Danio rerio)
Actinopterygii sycp2 31
  • 15 (a)
OneToOne
Species where no ortholog for SYCP2 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Eremothecium gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • Alpha proteobacteria (Wolbachia pipientis)
  • Amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • Baker's yeast (Saccharomyces cerevisiae)
  • Barley (Hordeum vulgare)
  • Beta proteobacteria (Neisseria meningitidis)
  • Bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • Common water flea (Daphnia pulex)
  • Corn (Zea mays)
  • E. coli (Escherichia coli)
  • Filamentous fungi (Aspergillus nidulans)
  • Firmicute Bacteria (Streptococcus pneumoniae)
  • Fission Yeast (Schizosaccharomyces pombe)
  • Fruit Fly (Drosophila melanogaster)
  • Green Algae (Chlamydomonas reinhardtii)
  • Honey Bee (Apis mellifera)
  • K. Lactis Yeast (Kluyveromyces lactis)
  • Loblloly Pine (Pinus taeda)
  • Malaria Parasite (Plasmodium falciparum)
  • Medicago Trunc (Medicago Truncatula)
  • Moss (Physcomitrella patens)
  • Orangutan (Pongo pygmaeus)
  • Pig (Sus scrofa)
  • Rainbow Trout (Oncorhynchus mykiss)
  • Rice (Oryza sativa)
  • Rice Blast Fungus (Magnaporthe grisea)
  • Schistosome Parasite (Schistosoma mansoni)
  • Sea Anemone (Nematostella vectensis)
  • Sea Vase (Ciona intestinalis)
  • Sea Squirt (Ciona savignyi)
  • Sea Urchin (Strongylocentrotus purpuratus)
  • Sorghum (Sorghum bicolor)
  • Soybean (Glycine max)
  • Stem Rust Fungus (Puccinia graminis)
  • Sugarcane (Saccharum officinarum)
  • Thale Cress (Arabidopsis thaliana)
  • Tomato (Lycopersicon esculentum)
  • Toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • Wheat (Triticum aestivum)
  • Worm (Caenorhabditis elegans)

Evolution for SYCP2 Gene

ENSEMBL:
Gene Tree for SYCP2 (if available)
TreeFam:
Gene Tree for SYCP2 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for SYCP2: view image

Paralogs for SYCP2 Gene

Paralogs for SYCP2 Gene

(1) SIMAP similar genes for SYCP2 Gene using alignment to 6 proteins:

  • SYCP2_HUMAN
  • A2A2M9_HUMAN
  • A2A340_HUMAN
  • A2A341_HUMAN
  • A6QL60_HUMAN
  • Q8IWA1_HUMAN

Pseudogenes.org Pseudogenes for SYCP2 Gene

genes like me logo Genes that share paralogs with SYCP2: view

Variants for SYCP2 Gene

Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for SYCP2 Gene

SNP ID Clinical significance and condition Chr 20 pos Variation AA Info Type
633612 Likely Pathogenic: Cryptozoospermia; Oligosynaptic infertility 59,880,446(-) TTTTTC/T FRAMESHIFT_VARIANT
633613 Likely Pathogenic: Cryptozoospermia; Oligosynaptic infertility 59,892,328(-) GTTCT/G FRAMESHIFT_VARIANT
633614 Likely Pathogenic: Early spermatogenesis maturation arrest; Oligosynaptic infertility 59,877,463(-) GTTTTT/G FRAMESHIFT_VARIANT
721877 Benign: not provided 59,867,813(-) G/A SYNONYMOUS_VARIANT
729423 Benign: not provided 59,880,392(-) A/G MISSENSE_VARIANT

Additional dbSNP identifiers (rs#s) for SYCP2 Gene

Structural Variations from Database of Genomic Variants (DGV) for SYCP2 Gene

Variant ID Type Subtype PubMed ID
dgv4335n100 CNV loss 25217958
dgv4336n100 CNV loss 25217958
dgv4337n100 CNV loss 25217958
nsv1062669 CNV loss 25217958
nsv1065994 CNV loss 25217958
nsv586370 CNV loss 21841781
nsv586371 CNV loss 21841781
nsv955145 CNV duplication 24416366

Variation tolerance for SYCP2 Gene

Residual Variation Intolerance Score: 96.5% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.49; 64.45% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for SYCP2 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SYCP2

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for SYCP2 Gene

Disorders for SYCP2 Gene

MalaCards: The human disease database

(5) MalaCards diseases for SYCP2 Gene - From: OMIM, GTR, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
spermatogenic failure 1
  • spgf1
tonsil squamous cell carcinoma
  • tonsillar squamous cell carcinoma
infertility
focal epithelial hyperplasia
  • heck disease
immunodeficiency-centromeric instability-facial anomalies syndrome
  • immune deficiency, variable, with centromeric instability of chromosomes 1, 9, and 16
- elite association - COSMIC cancer census association via MalaCards
Search SYCP2 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for SYCP2

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
Open Targets Platform
genes like me logo Genes that share disorders with SYCP2: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SYCP2 Gene

Publications for SYCP2 Gene

  1. Isolation and characterization of the human SCP2 cDNA and chromosomal localization of the gene. (PMID: 10341103) Schalk JA … Heyting C (Mammalian genome : official journal of the International Mammalian Genome Society 1999) 2 3 4
  2. Evaluation of 172 candidate polymorphisms for association with oligozoospermia or azoospermia in a large cohort of men of European descent. (PMID: 20378615) Aston KI … Carrell DT (Human reproduction (Oxford, England) 2010) 3 41
  3. The DNA sequence and comparative analysis of human chromosome 20. (PMID: 11780052) Deloukas P … Rogers J (Nature 2001) 3 4
  4. SCP2: a major protein component of the axial elements of synaptonemal complexes of the rat. (PMID: 9592139) Offenberg HH … Heyting C (Nucleic acids research 1998) 2 3
  5. SYCP2 Translocation-Mediated Dysregulation and Frameshift Variants Cause Human Male Infertility. (PMID: 31866047) Schilit SLP … Morton CC (American journal of human genetics 2020) 3

Products for SYCP2 Gene

Sources for SYCP2 Gene