Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases
Entrez ID	10388
Gene name	Synaptonemal complex protein 2
Gene symbol	SYCP2
Synonyms (NCBI Gene)	SCP-2SCP2SPGF1
Chromosome	20
Chromosome location	20q13.33
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

Show/Hide all (3)

SNP ID	Visualize variation	Clinical significance	Consequence
rs753462162	TTTTT>-,TTTT,TTTTTT	Pathogenic, likely-pathogenic	Intron variant, coding sequence variant, frameshift variant, genic downstream transcript variant
rs1600840291	CTTTT>-	Likely-pathogenic, pathogenic	Coding sequence variant, genic downstream transcript variant, frameshift variant
rs1600877766	TCTT>-	Likely-pathogenic, pathogenic	Coding sequence variant, frameshift variant

Show/Hide all (14)

miRTarBase ID	miRNA	Experiments
MIRT1405110	hsa-miR-1304	CLIP-seq
MIRT1405111	hsa-miR-142-5p	CLIP-seq
MIRT1405112	hsa-miR-337-3p	CLIP-seq
MIRT1405113	hsa-miR-340	CLIP-seq
MIRT1405114	hsa-miR-3977	CLIP-seq
MIRT1405115	hsa-miR-4691-5p	CLIP-seq
MIRT1405116	hsa-miR-4775	CLIP-seq
MIRT1405117	hsa-miR-4789-5p	CLIP-seq
MIRT1405118	hsa-miR-617	CLIP-seq
MIRT1405119	hsa-miR-935	CLIP-seq
MIRT2121537	hsa-miR-3117-3p	CLIP-seq
MIRT2121538	hsa-miR-3169	CLIP-seq
MIRT2121539	hsa-miR-4759	CLIP-seq
MIRT2343594	hsa-miR-28-3p	CLIP-seq

Show/Hide all (24)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000779	Component	Condensed chromosome, centromeric region	IBA
GO:0000795	Component	Synaptonemal complex	IEA
GO:0000795	Component	Synaptonemal complex	NAS	10341103
GO:0000800	Component	Lateral element	IBA
GO:0000800	Component	Lateral element	IEA
GO:0000800	Component	Lateral element	ISS
GO:0003677	Function	DNA binding	IEA
GO:0003677	Function	DNA binding	NAS	10341103
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	NAS	10341103
GO:0005694	Component	Chromosome	IEA
GO:0006915	Process	Apoptotic process	IEA
GO:0007130	Process	Synaptonemal complex assembly	NAS	10341103
GO:0007140	Process	Male meiotic nuclear division	IEA
GO:0007143	Process	Female meiotic nuclear division	IEA
GO:0009566	Process	Fertilization	IEA
GO:0009887	Process	Animal organ morphogenesis	IEA
GO:0035234	Process	Ectopic germ cell programmed cell death	IEA
GO:0043066	Process	Negative regulation of apoptotic process	IEA
GO:0048808	Process	Male genitalia morphogenesis	IEA
GO:0051093	Process	Negative regulation of developmental process	IEA
GO:0051301	Process	Cell division	IEA
GO:0051321	Process	Meiotic cell cycle	IEA
GO:2000242	Process	Negative regulation of reproductive process	IEA

MIM	HGNC	e!Ensembl
604105	11490	ENSG00000196074

Q9BX26

Protein name

Synaptonemal complex protein 2 (SCP-2) (Synaptonemal complex lateral element protein) (hsSCP2)

Protein 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 develop

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF18581	SYCP2_ARLD	10 → 184	Synaptonemal complex 2 armadillo-repeat-like domain	Domain
PF18584	SYCP2_SLD	278 → 390	Synaptonemal complex 2 Spt16M-like domain	Domain

Sequence

MPIRPDLQQLEKCIDDALRKNDFKPLKTLLQIDICEDVKIKCSKQFFHKVDNLICRELNK
EDIHNVSAILVSVGRCGKNISVLGQAGLLTMIKQGLIQKMVAWFEKSKDIIQSQGNSKDE
AVLNMIEDLVDLLLVIHDVSDEGKKQVVESFVPRICSLVIDSRVNICIQQEIIKKMNAML
DKMPQDARKILSNQEMLILMSSMGERILDAGDYDLQVGIVEALCRMTTEKQRQELAHQWF
SMDFIAKAFKRIKDSEFETDCRIFLNLVNGMLGDKRRVFTFPCLSAFLDKYELQIPSDEK
LEEFWIDFNLGSQTLSFYIAGDNDDHQWEAVTVPEEKVQIYSIEVRESKKLLTIILKNTV
KISKREGKELLLYFDASLEITNVTQKIFGATKHRESIRKQGISVAKTSLHILFDASGSQI
LVPESQISPVGEELVSLKEKSKSPKEFAKPSKYIKNSDKGNRNNSQLEKTTPSKRKMSEA
SMIVSGADRYTMRSPVLFSNTSIPPRRRRIKPPLQMTSSAEKPSVSQTSENRVDNAASLK
SRSSEGRHRRDNIDKHIKTAKCVENTENKNVEFPNQNFSELQDVIPDSQAAEKRDHTILP
GVLDNICGNKIHSKWACWTPVTNIELCNNQRASTSSGDTLNQDIVINKKLTKQKSSSSIS
DHNSEGTGKVKYKKEQTDHIKIDKAEVEVCKKHNQQQNHPKYSGQKNTENAKQSDWPVES
ETTFKSVLLNKTIEESLIYRKKYILSKDVNTATCDKNPSASKNVQSHRKAEKELTSELNS
WDSKQKKMREKSKGKEFTNVAESLISQINKRYKTKDDIKSTRKLKESLINSGFSNKPVVQ
LSKEKVQKKSYRKLKTTFVNVTSECPVNDVYNFNLNGADDPIIKLGIQEFQATAKEACAD
RSIRLVGPRNHDELKSSVKTKDKKIITNHQKKNLFSDTETEYRCDDSKTDISWLREPKSK
PQLIDYSRNKNVKNHKSGKSRSSLEKGQPSSKMTPSKNITKKMDKTIPEGRIRLPRKATK
TKKNYKDLSNSESECEQEFSHSFKENIPVKEENIHSRMKTVKLPKKQQKVFCAETEKELS
KQWKNSSLLKDAIRDNCLDLSPRSLSGSPSSIEVTRCIEKITEKDFTQDYDCITKSISPY
PKTSSLESLNSNSGVGGTIKSPKNNEKNFLCASESCSPIPRPLFLPRHTPTKSNTIVNRK
KISSLVLTQETQNSNSYSDVSSYSSEERFMEIESPHINENYIQSKREESHLASSLSKSSE
GREKTWFDMPCDATHVSGPTQHLSRKRIYIEDNLSNSNEVEMEEKGERRANLLPKKLCKI
EDADHHIHKMSESVSSLSTNDFSIPWETWQNEFAGIEMTYETYERLNSEFKRRNNIRHKM
LSYFTTQSWKTAQQHLRTMNHQSQDSRIKKLDKFQFIIIEELENFEKDSQSLKDLEKEFV
DFWEKIFQKFSAYQKSEQQRLHLLKTSLAKSVFCNTDSEETVFTSEMCLMKEDMKVLQDR
LLKDMLEEELLNVRRELMSVFMSHERNANV

Sequence length

1530

Interactions

View interactions

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 (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Cryptozoospermia	Likely pathogenic; Pathogenic	rs1600840291, rs1600877766	RCV000855716 RCV000855717	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Male infertility with azoospermia or oligozoospermia due to single gene mutation	Likely pathogenic	rs2517469276	RCV003991629	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Non-obstructive azoospermia	Likely pathogenic; Pathogenic	rs1600840291, rs1600877766, rs753462162	RCV001644818 RCV001644819 RCV001644820	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Oligosynaptic infertility	Likely pathogenic; Pathogenic	rs2517481810, rs1600840291, rs1600877766, rs753462162	RCV003990189 RCV001005041 RCV001005042 RCV001005040	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Spermatocyte maturation arrest	Likely pathogenic; Pathogenic	rs753462162	RCV000855718	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (15)

Phenotype Name	Clinical Significance	Source	Evidence Score
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.
Cervical cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Clear cell carcinoma of kidney	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRYPTOSPERMIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hepatocellular carcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of urinary bladder	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Prostate cancer	Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Uncertain significance; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SPERMATOGENIC FAILURE 1	—	Disgenet, HPO Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SYCP2-related disorder	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TESTICULAR AZOOSPERMIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (13)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
Arrest of spermatogenesis	Associate	31866047	★★★★★ ★☆☆☆☆ Found in Text Mining only
Azoospermia	Associate	31866047	★★★★★ ★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Stimulate	36689258	★★★★★ ★☆☆☆☆ Found in Text Mining only
Chromosome Aberrations	Associate	31866047	★★★★★ ★☆☆☆☆ Found in Text Mining only
Diabetes Gestational	Associate	36698149	★★★★★ ★☆☆☆☆ Found in Text Mining only
Immunodeficiency syndrome variable	Associate	26161907	★★★★★ ★☆☆☆☆ Found in Text Mining only
Infertility Male	Associate	31866047, 39202451	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	26334652, 36689258	★★★★★ ★☆☆☆☆ Found in Text Mining only
Oligospermia	Associate	31866047	★★★★★ ★☆☆☆☆ Found in Text Mining only
Oropharyngeal Neoplasms	Associate	26334652	★★★★★ ★☆☆☆☆ Found in Text Mining only
Papillomavirus Infections	Associate	32164487	★★★★★ ★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Associate	17079134, 36142875	★★★★★ ★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Associate	23405241	★★★★★ ★☆☆☆☆ Found in Text Mining only

SYCP2 (synaptonemal complex protein 2)