SYCP3 (synaptonemal complex protein 3)

Gene Gene information from NCBI Gene database.
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID 50511
Gene name Synaptonemal complex protein 3
Gene symbol SYCP3
Synonyms (NCBI Gene)
COR1RPRGL4SCP3SPGF4
Chromosome 12
Chromosome location 12q23.2
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
miRNA miRNA information provided by mirtarbase database.
2
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all (2)
miRTarBase ID miRNA Experiments Reference
MIRT1405127 hsa-miR-1279 CLIP-seq
MIRT1405128 hsa-miR-487a CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
16
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Show/Hide all (16)
GO ID Ontology Definition Evidence Reference
GO:0000775 Component Chromosome, centromeric region IEA
GO:0000775 Component Chromosome, centromeric region ISS
GO:0000795 Component Synaptonemal complex IBA
GO:0000795 Component Synaptonemal complex IDA 9774970
GO:0000800 Component Lateral element ISS
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
MIM HGNC e!Ensembl
604759 18130 ENSG00000139351
Protein Protein information from UniProt database.
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
Q8IZU3
Protein name Synaptonemal complex protein 3 (SCP-3)
Protein function Component of the synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Required for centromere pairing during meiosis in male germ cells (By similarity). Required for normal meiosis during spermatogenesis a
PDB 4CPC
Family and domains

Pfam

Accession ID Position in sequence Description Type
PF04803 Cor1 83 → 214 Cor1/Xlr/Xmr conserved region Coiled-coil
Tissue specificity TISSUE SPECIFICITY: Testis-specific. {ECO:0000269|PubMed:12213195, ECO:0000269|PubMed:14643120}.
Sequence 
MVSSGKKYSRKSGKPSVEDQFTRAYDFETEDKKDLSGSEEDVIEGKTAVIEKRRKKRSSA
GVVEDMGGEVQNMLEGVGVDINKALLAKRKRLEMYTKASLKTSNQKIEHVWKTQQDQRQK
LNQEYSQQFLTLFQQWDLDMQKAEEQEEKILNMFRQQQKILQQSRIVQSQRLKTIKQLYE
QFIKSMEELEKNHDNLLTGAQNEFKKEMAMLQKKIMMETQQQEIASVRKSLQSMLF
Sequence length 236
Interactions View interactions
Pathways Pathway information has different metabolic/signaling pathways associated with genes.
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
  KEGG 
  Homologous recombination  
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
7
Gene miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Show/Hide Causal Diseases (2)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Gastric cancer Pathogenic rs769825641 RCV005887319
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spermatogenic failure 4 Pathogenic rs761136347, rs587776620, rs769825641 RCV000005702
RCV000005703
RCV000005704
★★★★★
★★★★☆
ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Show/Hide Unknown Diseases (5)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
AZOOSPERMIA — CTD, Disgenet
CTD, Disgenet
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
INFERTILITY DISORDER — GWAS catalog
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Male infertility Uncertain significance ClinVar
Disgenet
★★★★★
★★★☆☆
Reported in Unknown/Other Associations (≥2 sources)
MALE INFERTILITY WITH AZOOSPERMIA OR OLIGOZOOSPERMIA DUE TO SINGLE GENE MUTATION — Orphanet
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Show/Hide Text Mining Associations (35)
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acute monocytic leukemia Monocytic Leukemia BEFREE 12681366
★★★★★
★☆☆☆☆
Found in Text Mining only
Azoospermia Azoospermia BEFREE 14643120, 16213863, 16227348
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Azoospermia Azoospermia CTD_human_DG 14643120
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Azoospermia Azoospermia Pubtator 19110213 Associate
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Azoospermia Azoospermia HPO_DG
★★★★★
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Azoospermia Nonobstructive Nonobstructive azoospermia Pubtator 16824523 Associate
★★★★★
★☆☆☆☆
Found in Text Mining only
Azoospermia, Nonobstructive Azoospermia BEFREE 16824523, 22670862
★★★★★
★☆☆☆☆
Found in Text Mining only
Carcinoma of lung Lung carcinoma BEFREE 28623914
★★★★★
★☆☆☆☆
Found in Text Mining only
cervical cancer Cervical Cancer BEFREE 24905095
★★★★★
★☆☆☆☆
Found in Text Mining only
Cervical Intraepithelial Neoplasia Cervical Intraepithelial Neoplasia BEFREE 24905095
★★★★★
★☆☆☆☆
Found in Text Mining only