SYCE1 (synaptonemal complex central element protein 1)

Gene

• Entrez ID: 93426
• Gene name: Synaptonemal complex central element protein 1
• Gene symbol: SYCE1
• Synonyms (NCBI Gene): C10orf94, CT76, POF12, SPGF15
• Chromosome: 10
• Chromosome location: 10q26.3
• Summary: This gene encodes a member of the synaptonemal complex, which links homologous chromosomes during prophase I of meiosis. The tripartite structure of the complex is highly conserved amongst metazoans. It consists of two lateral elements and a central regio

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs774225566	T>C	Pathogenic	Splice acceptor variant
rs875989885	G>A	Pathogenic	Stop gained, coding sequence variant
rs1589966038	CT>-	Pathogenic	Frameshift variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT038278	hsa-miR-26a-2-3p	CLASH	23622248
MIRT1405072	hsa-miR-23a	CLIP-seq
MIRT1405073	hsa-miR-23b	CLIP-seq
MIRT1405074	hsa-miR-23c	CLIP-seq
MIRT1405075	hsa-miR-3130-3p	CLIP-seq
MIRT1405076	hsa-miR-3185	CLIP-seq
MIRT1405077	hsa-miR-4325	CLIP-seq
MIRT1405078	hsa-miR-4474-5p	CLIP-seq
MIRT1405079	hsa-miR-4659a-5p	CLIP-seq
MIRT1405080	hsa-miR-4659b-5p	CLIP-seq
MIRT1405081	hsa-miR-4716-5p	CLIP-seq
MIRT1405082	hsa-miR-4717-3p	CLIP-seq
MIRT1405083	hsa-miR-4776-3p	CLIP-seq
MIRT1405084	hsa-miR-4793-3p	CLIP-seq
MIRT1405085	hsa-miR-5096	CLIP-seq
MIRT1405086	hsa-miR-544	CLIP-seq
MIRT1405087	hsa-miR-4704-3p	CLIP-seq
MIRT1405088	hsa-miR-4705	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000795	Component	Synaptonemal complex	IBA
GO:0000795	Component	Synaptonemal complex	IEA
GO:0000801	Component	Central element	IEA
GO:0000801	Component	Central element	ISS	15944401
GO:0005515	Function	Protein binding	IPI	25416956, 25910212, 26871637, 27107012, 31515488, 32296183, 33961781, 36217029
GO:0005634	Component	Nucleus	IEA
GO:0005694	Component	Chromosome	IEA
GO:0005694	Component	Chromosome	ISS
GO:0007130	Process	Synaptonemal complex assembly	IC	15944401
GO:0007130	Process	Synaptonemal complex assembly	IEA
GO:0051301	Process	Cell division	IEA
GO:0051321	Process	Meiotic cell cycle	IEA
GO:0070193	Process	Synaptonemal complex organization	IEA

Other IDs

• MIM: 611486
• HGNC: 28852
• e!Ensembl: ENSG00000171772

Protein

• UniProt ID: Q8N0S2
• Protein name: Synaptonemal complex central element protein 1 (Cancer/testis antigen 76) (CT76)
• Protein function: Major component of the transverse central element of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase. Requires SYCP1 in order to be incorporated into the central element. May have a role in the synapto
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF15233	SYCE1	47 → 198	Synaptonemal complex central element protein 1	Coiled-coil

• Sequence:

  MAGRSLTSKAEPTAGAVDRAEKAGGQDTSSQKIEDLMEMVQKLQKVGSLEPRVEVLINRI
  NEVQQAKKKANKDLGEARTICEALQKELDSLHGEKVHLKEILSKKQETLRILRLHCQEKE
  SEAHRKHTMLQECKERISALNLQIEEEKNKQRQLRLAFEEQLEDLMGQHKDLWDFHMPER
  LAKEICALDSSKEQLLKEEKLVKATLEDVKHQLCSLCGAEGPSTLDEGLFLRSQEAAATV
  QLFQEEHRKAEELLAAAAQRHQQLQQKCQQQQQKRQRLKEELEKHGMQVPAQAQSTQEEE
  AGPGDVASPKPLKGERPGAAHQAGPDVLIGQEDTLHPDLSPRGFQEIKELF

• Sequence length: 351

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)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Premature ovarian failure 12	Pathogenic	rs875989885	RCV000211464	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spermatogenic failure 15	Pathogenic	rs774225566	RCV000211704	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
MALE INFERTILITY WITH AZOOSPERMIA OR OLIGOZOOSPERMIA DUE TO SINGLE GENE MUTATION	—	Disgenet, GWAS catalog, Orphanet Disgenet, GWAS catalog, Orphanet Disgenet, GWAS catalog, Orphanet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYCE1-related disorder	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Age related macular degeneration	Age-related macular degeneration	HPO_DG			★☆☆☆☆ Found in Text Mining only
Azoospermia	Azoospermia	Pubtator	25899990, 33728612, 35023261, 35366911, 35413094, 35718780	Associate	★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	39208330	Associate	★☆☆☆☆ Found in Text Mining only
Down Syndrome	Down syndrome	Pubtator	35718780	Associate	★☆☆☆☆ Found in Text Mining only
Infertility	Infertility	Pubtator	33823999	Associate	★☆☆☆☆ Found in Text Mining only
Infertility Male	Male infertility	Pubtator	34954426, 35023261, 35718780	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	GWASCAT_DG	27903959		★☆☆☆☆ Found in Text Mining only
Male infertility with azoospermia or oligozoospermia due to single gene mutation	Male infertility	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Microphthalmos	Microphthalmos	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nasopharyngeal Carcinoma	Nasopharyngeal carcinoma	Pubtator	19805575	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	24970476		★☆☆☆☆ Found in Text Mining only
NON RARE IN EUROPE: Primary ovarian failure	Ovarian Failure	Orphanet			★☆☆☆☆ Found in Text Mining only
Non-obstructive azoospermia	Non-obstructive azoospermia	BEFREE	25899990		★☆☆☆☆ Found in Text Mining only
Non-obstructive azoospermia	Non-obstructive azoospermia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Obstructive azoospermia	Obstructive azoospermia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ovarian Dysgenesis 2	Ovarian dysgenesis	Pubtator	21256485	Associate	★☆☆☆☆ Found in Text Mining only
Ovarian Failure, Premature	Ovarian Failure	BEFREE	25062452, 27301361		★☆☆☆☆ Found in Text Mining only
Premature Menopause	Premature Menopause	BEFREE	25062452, 27301361		★☆☆☆☆ Found in Text Mining only
PREMATURE OVARIAN FAILURE 12	Premature Ovarian Failure	CTD_human_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PREMATURE OVARIAN FAILURE 12	Premature Ovarian Failure	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Primary physiologic amenorrhea	Physiologic Amenorrhea	HPO_DG			★☆☆☆☆ Found in Text Mining only
SPERMATOGENIC FAILURE 15	Spermatogenic Failure	CTD_human_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
SPERMATOGENIC FAILURE 15	Spermatogenic Failure	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Testicular Diseases	Testicular disease	Pubtator	33728612	Associate	★☆☆☆☆ Found in Text Mining only
Testicular Neoplasms	Testicular neoplasm	Pubtator	39208330	Associate	★☆☆☆☆ Found in Text Mining only
Trichohepatoenteric Syndrome	Trichohepatoenteric Syndrome	BEFREE	24742017		★☆☆☆☆ Found in Text Mining only