SYCP1 (synaptonemal complex protein 1)

Gene

• Entrez ID: 6847
• Gene name: Synaptonemal complex protein 1
• Gene symbol: SYCP1
• Synonyms (NCBI Gene): CT8, HOM-TES-14, SCP-1, SCP1
• Chromosome: 1
• Chromosome location: 1p13.2

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT054241	hsa-miR-124-3p	Flow cytometry, In situ hybridization, Luciferase reporter assay, qRT-PCR, Western blot	23548312
MIRT054241	hsa-miR-124-3p	Luciferase reporter assay	23313552
MIRT438804	hsa-miR-96-5p	Luciferase reporter assay	23313552
MIRT054241	hsa-miR-124-3p	Luciferase reporter assay	23313552
MIRT438804	hsa-miR-96-5p	Luciferase reporter assay	23313552
MIRT2121533	hsa-miR-1179	CLIP-seq
MIRT2121534	hsa-miR-1264	CLIP-seq
MIRT2121535	hsa-miR-4719	CLIP-seq
MIRT2121536	hsa-miR-586	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000711	Process	Meiotic DNA repair synthesis	IBA
GO:0000711	Process	Meiotic DNA repair synthesis	IEA
GO:0000775	Component	Chromosome, centromeric region	IEA
GO:0000794	Component	Condensed nuclear chromosome	IEA
GO:0000795	Component	Synaptonemal complex	IEA
GO:0000795	Component	Synaptonemal complex	ISS
GO:0000801	Component	Central element	IBA
GO:0000801	Component	Central element	IEA
GO:0000802	Component	Transverse filament	IBA
GO:0000802	Component	Transverse filament	IEA
GO:0001673	Component	Male germ cell nucleus	IBA
GO:0001673	Component	Male germ cell nucleus	IEA
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	TAS	1464329
GO:0003690	Function	Double-stranded DNA binding	IBA
GO:0003690	Function	Double-stranded DNA binding	IDA	29915389
GO:0005634	Component	Nucleus	IEA
GO:0005694	Component	Chromosome	IEA
GO:0005694	Component	Chromosome	ISS
GO:0007129	Process	Homologous chromosome pairing at meiosis	IEA
GO:0007129	Process	Homologous chromosome pairing at meiosis	ISS
GO:0007130	Process	Synaptonemal complex assembly	IEA
GO:0007130	Process	Synaptonemal complex assembly	ISS	15944401
GO:0007131	Process	Reciprocal meiotic recombination	IEA
GO:0007131	Process	Reciprocal meiotic recombination	ISS
GO:0007131	Process	Reciprocal meiotic recombination	TAS	1464329
GO:0007283	Process	Spermatogenesis	IEA
GO:0007283	Process	Spermatogenesis	TAS	1464329
GO:0030849	Component	Autosome	IEA
GO:0032880	Process	Regulation of protein localization	IEA
GO:0035092	Process	Sperm DNA condensation	IEA
GO:0051026	Process	Chiasma assembly	IBA
GO:0051026	Process	Chiasma assembly	IEA
GO:0051289	Process	Protein homotetramerization	IDA	29915389
GO:0051301	Process	Cell division	IEA
GO:0051321	Process	Meiotic cell cycle	IEA
GO:0051878	Process	Lateral element assembly	IBA
GO:0051878	Process	Lateral element assembly	IEA

Other IDs

• MIM: 602162
• HGNC: 11487
• e!Ensembl: ENSG00000198765

Protein

• UniProt ID: Q15431
• Protein name: Synaptonemal complex protein 1 (SCP-1) (Cancer/testis antigen 8) (CT8)
• Protein function: Major component of the transverse filaments of synaptonemal complexes, formed between homologous chromosomes during meiotic prophase. Required for normal assembly of the central element of the synaptonemal complexes. Required for normal centrome
• PDB: 4YTO, 6F5X, 6F62, 6F63, 6F64
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF05483	SCP-1	28 → 792	Synaptonemal complex protein 1 (SCP-1)	Coiled-coil

• Tissue specificity: TISSUE SPECIFICITY: Testis. {ECO:0000269|PubMed:9371398}.
• Sequence:

  MEKQKPFALFVPPRSSSSQVSAVKPQTLGGDSTFFKSFNKCTEDDFEFPFAKTNLSKNGE
  NIDSDPALQKVNFLPVLEQVGNSDCHYQEGLKDSDLENSEGLSRVYSKLYKEAEKIKKWK
  VSTEAELRQKESKLQENRKIIEAQRKAIQELQFGNEKVSLKLEEGIQENKDLIKENNATR
  HLCNLLKETCARSAEKTKKYEYEREETRQVYMDLNNNIEKMITAFEELRVQAENSRLEMH
  FKLKEDYEKIQHLEQEYKKEINDKEKQVSLLLIQITEKENKMKDLTFLLEESRDKVNQLE
  EKTKLQSENLKQSIEKQHHLTKELEDIKVSLQRSVSTQKALEEDLQIATKTICQLTEEKE
  TQMEESNKARAAHSFVVTEFETTVCSLEELLRTEQQRLEKNEDQLKILTMELQKKSSELE
  EMTKLTNNKEVELEELKKVLGEKETLLYENKQFEKIAEELKGTEQELIGLLQAREKEVHD
  LEIQLTAITTSEQYYSKEVKDLKTELENEKLKNTELTSHCNKLSLENKELTQETSDMTLE
  LKNQQEDINNNKKQEERMLKQIENLQETETQLRNELEYVREELKQKRDEVKCKLDKSEEN
  CNNLRKQVENKNKYIEELQQENKALKKKGTAESKQLNVYEIKVNKLELELESAKQKFGEI
  TDTYQKEIEDKKISEENLLEEVEKAKVIADEAVKLQKEIDKRCQHKIAEMVALMEKHKHQ
  YDKIIEERDSELGLYKSKEQEQSSLRASLEIELSNLKAELLSVKKQLEIEREEKEKLKRE
  AKENTATLKEKKDKKTQTFLLETPEIYWKLDSKAVPSQTVSRNFTSVDHGISKDKRDYLW
  TSAKNTLSTPLPKAYTVKTPTKPKLQQRENLNIPIEESKKKRKMAFEFDINSDSSETTDL
  LSMVSEEETLKTLYRNNNPPASHLCVKTPKKAPSSLTTPGSTLKFGAIRKMREDRWAVIA
  KMDRKKKLKEAEKLFV

• Sequence length: 976

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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Mycotic Aneurysm, Intracranial	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PANCREATIC NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adenocarcinoma	Adenocarcinoma	CTD_human_DG	14991579		★☆☆☆☆ Found in Text Mining only
Adenocarcinoma, Basal Cell	Adenocarcinoma	CTD_human_DG	14991579		★☆☆☆☆ Found in Text Mining only
Adenocarcinoma, Oxyphilic	Adenocarcinoma	CTD_human_DG	14991579		★☆☆☆☆ Found in Text Mining only
Adenocarcinoma, Tubular	Adenocarcinoma	CTD_human_DG	14991579		★☆☆☆☆ Found in Text Mining only
Azoospermia, Nonobstructive	Azoospermia	BEFREE	22670862		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	24806942		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	11531257	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	9560255	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma, Cribriform	Carcinoma	CTD_human_DG	14991579		★☆☆☆☆ Found in Text Mining only
Carcinoma, Granular Cell	Carcinoma	CTD_human_DG	14991579		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	15756003, 39208330	Associate	★☆☆☆☆ Found in Text Mining only
Conventional (Clear Cell) Renal Cell Carcinoma	Renal Carcinoma	BEFREE	25293974		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	9560255	Associate	★☆☆☆☆ Found in Text Mining only
Hereditary Breast and Ovarian Cancer Syndrome	Hereditary breast and ovarian cancer syndrome	Pubtator	9560255	Associate	★☆☆☆☆ Found in Text Mining only
Hyperglycemia	Hyperglycemia	BEFREE	30529353		★☆☆☆☆ Found in Text Mining only
Infertility	Infertility	Pubtator	18706547	Associate	★☆☆☆☆ Found in Text Mining only
Intracranial Aneurysm	Intracranial aneurysm	Pubtator	35228681	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia Myeloid Acute	Myeloid leukemia	Pubtator	21898529	Associate	★☆☆☆☆ Found in Text Mining only
Leukemia, Myelocytic, Acute	Leukemia	BEFREE	10584877		★☆☆☆☆ Found in Text Mining only
Lymphoma, T-Cell, Cutaneous	Lymphoma	BEFREE	11149944, 11807795		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of liver	Liver Cancer	BEFREE	25893300		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of pancreas	Pancreatic cancer	CTD_human_DG	14991579		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of testis	Malignant Neoplasm Of Testis	BEFREE	14991579, 15672408, 16094643		★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	BEFREE	10584877		★☆☆☆☆ Found in Text Mining only
Multiple Myeloma	Multiple myeloma	Pubtator	10584877	Associate	★☆☆☆☆ Found in Text Mining only
Mycosis Fungoides	Mycosis fungoides	Pubtator	25779945	Associate	★☆☆☆☆ Found in Text Mining only
Myeloid Leukemia, Chronic	Myeloid Leukemia	BEFREE	10584877		★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	11149944, 12584747, 25293974, 25893300, 28440748		★☆☆☆☆ Found in Text Mining only
Pancreatic carcinoma	Pancreatic carcinoma	BEFREE	14991579		★☆☆☆☆ Found in Text Mining only
Pancreatic Neoplasm	Pancreatic Neoplasm	CTD_human_DG	14991579		★☆☆☆☆ Found in Text Mining only
Pancreatitis, Chronic	Pancreatitis	BEFREE	14991579		★☆☆☆☆ Found in Text Mining only
Parapsoriasis	Parapsoriasis	BEFREE	11807795		★☆☆☆☆ Found in Text Mining only
Sezary Syndrome	Sezary syndrome	Pubtator	25779945	Associate	★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	16929165	Associate	★☆☆☆☆ Found in Text Mining only
Stomach Neoplasms	Stomach neoplasms	Pubtator	11531257	Stimulate	★☆☆☆☆ Found in Text Mining only
SVEINSSON CHORIORETINAL ATROPHY	Sveinsson Chorioretinal Atrophy	BEFREE	28684768		★☆☆☆☆ Found in Text Mining only
synovial sarcoma	Synovial sarcoma	BEFREE	11454979		★☆☆☆☆ Found in Text Mining only
Testicular Germ Cell Tumor	Testicular germ cell tumor	Pubtator	11454979	Associate	★☆☆☆☆ Found in Text Mining only
Testicular Neoplasms	Testicular neoplasm	Pubtator	16030183, 39208330	Associate	★☆☆☆☆ Found in Text Mining only
Xeroderma Pigmentosum	Xeroderma Pigmentosum	BEFREE	11454979		★☆☆☆☆ Found in Text Mining only