SYCP2 (synaptonemal complex protein 2)

Gene

• Entrez ID: 10388
• Gene name: Synaptonemal complex protein 2
• Gene symbol: SYCP2
• Synonyms (NCBI Gene): SCP-2, SCP2, SPGF1
• 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

SNPs

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

miRNA

miRTarBase ID	miRNA	Experiments	Reference
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

Gene ontology (GO)

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

Other IDs

• MIM: 604105
• HGNC: 11490
• e!Ensembl: ENSG00000196074

Protein

• UniProt ID: 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

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
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)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
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

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acquired Polyneuropathy	Polyneuropathy	CTD_human_DG	16685654		★☆☆☆☆ Found in Text Mining only
Adrenocortical carcinoma	Adrenocortical carcinoma	BEFREE	8640304		★☆☆☆☆ Found in Text Mining only
Adrenoleukodystrophy	Adrenoleukodystrophy	Pubtator	2085845	Associate	★☆☆☆☆ Found in Text Mining only
Arrhythmias Cardiac	Cardiac arrhythmias	Pubtator	35996156	Inhibit	★☆☆☆☆ Found in Text Mining only
Arteriosclerosis	Arteriosclerosis	BEFREE	29700117		★☆☆☆☆ Found in Text Mining only
Arthritis Psoriatic	Psoriatic arthritis	Pubtator	34344401	Associate	★☆☆☆☆ Found in Text Mining only
Atherosclerosis	Atherosclerosis	BEFREE	29700117		★☆☆☆☆ Found in Text Mining only
Azoospermia	Azoospermia	Pubtator	31866047, 35996156	Associate	★☆☆☆☆ Found in Text Mining only
Azoospermia	Azoospermia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Azoospermia, Nonobstructive	Azoospermia	BEFREE	22670862		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	22995475, 30221688, 30511892		★☆☆☆☆ Found in Text Mining only
Breast Neoplasms	Breast neoplasm	Pubtator	28758931, 37511575	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	37304236	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Squamous Cell	Squamous cell carcinoma	Pubtator	36689258	Stimulate	★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	30221688		★☆☆☆☆ Found in Text Mining only
cervical cancer	Cervical Cancer	BEFREE	23405241		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervix carcinoma	Cervix carcinoma	BEFREE	23405241		★☆☆☆☆ Found in Text Mining only
Childhood Ataxia with Central Nervous System Hypomyelinization	Leukoencephalopathy with vanishing white matter	CTD_human_DG	16685654		★☆☆☆☆ Found in Text Mining only
Cholangiocarcinoma	Cholangiocarcinoma	Pubtator	34211100	Associate	★☆☆☆☆ Found in Text Mining only
Cholesterol gallstones	Cholesterol gallstones	BEFREE	15730934, 21310066		★☆☆☆☆ Found in Text Mining only
Congenital contractural arachnodactyly	Congenital Contractural Arachnodactyly	BEFREE	31177590		★☆☆☆☆ Found in Text Mining only
Congenital pectus carinatum	Congenital Pectus Carinatum	BEFREE	31434294		★☆☆☆☆ Found in Text Mining only
Connective Tissue Diseases	Connective Tissue Disease	BEFREE	27863214		★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	33157955	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Gestational	Gestational diabetes	Pubtator	36698149	Associate	★☆☆☆☆ Found in Text Mining only
Diabetes Mellitus	Diabetes mellitus	Pubtator	37511575	Associate	★☆☆☆☆ Found in Text Mining only
Dyslipidemias	Dyslipidemias	BEFREE	29700117		★☆☆☆☆ Found in Text Mining only
Dystonia Disorders	Dystonia	BEFREE	16685654		★☆☆☆☆ Found in Text Mining only
Fatty Liver	Fatty Liver	BEFREE	19289417, 27940000, 28411199		★☆☆☆☆ Found in Text Mining only
Gallstones	Gallstones	Pubtator	21310066	Stimulate	★☆☆☆☆ Found in Text Mining only
Growth Disorders	Growth disorder	Pubtator	33157955	Associate	★☆☆☆☆ Found in Text Mining only
Hearing Loss	Hearing loss	Pubtator	33713422	Associate	★☆☆☆☆ Found in Text Mining only
Hypercholesterolemia	Hypercholesterolemia	BEFREE	31519191		★☆☆☆☆ Found in Text Mining only
Hyperglycemia	Hyperglycemia	BEFREE	30529353		★☆☆☆☆ Found in Text Mining only
Infantile neuronal ceroid lipofuscinosis	Neuronal Ceroid Lipofuscinosis	BEFREE	8004106		★☆☆☆☆ Found in Text Mining only
Infertility Male	Male infertility	Pubtator	31866047, 39202451	Associate	★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	33157955	Associate	★☆☆☆☆ Found in Text Mining only
Leukoencephalopathy	Leukoencephalopathy	CTD_human_DG	16685654		★☆☆☆☆ Found in Text Mining only
Leukoencephalopathy	Leukoencephalopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
LEUKOENCEPHALOPATHY WITH DYSTONIA AND MOTOR NEUROPATHY	Leukoencephalopathy With Dystonia And Motor Neuropathy	GENOMICS_ENGLAND_DG	16685654, 26497993		★☆☆☆☆ Found in Text Mining only
LEUKOENCEPHALOPATHY WITH DYSTONIA AND MOTOR NEUROPATHY	Leukoencephalopathy With Dystonia And Motor Neuropathy	ORPHANET_DG	16685654		★☆☆☆☆ Found in Text Mining only
LEUKOENCEPHALOPATHY WITH DYSTONIA AND MOTOR NEUROPATHY	Leukoencephalopathy With Dystonia And Motor Neuropathy	CTD_human_DG			★☆☆☆☆ Found in Text Mining only
LEUKOENCEPHALOPATHY WITH DYSTONIA AND MOTOR NEUROPATHY	Leukoencephalopathy With Dystonia And Motor Neuropathy	CLINVAR_DG			★☆☆☆☆ Found in Text Mining only
Leukoencephalopathy-dystonia-motor neuropathy syndrome	Leukoencephalopathy With Dystonia And Motor Neuropathy	Orphanet			★☆☆☆☆ Found in Text Mining only
Lipoid congenital adrenal hyperplasia	Congenital lipoid adrenal hyperplasia	Pubtator	1661294	Associate	★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	BEFREE	22995475, 30221688, 30511892		★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	UNIPROT_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of ovary	Ovarian cancer	BEFREE	30221688		★☆☆☆☆ Found in Text Mining only
Malignant tumor of cervix	Cervical Tumor	BEFREE	23405241		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	Pubtator	33157955	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	30221688		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Neurodegenerative disorder	Pubtator	35996156	Associate	★☆☆☆☆ Found in Text Mining only
Neurodegenerative Disorders	Neurodegenerative Disorders	BEFREE	8004106		★☆☆☆☆ Found in Text Mining only
Non-alcoholic Fatty Liver Disease	Non-Alcoholic Fatty Liver Disease	BEFREE	28012135, 29307784		★☆☆☆☆ Found in Text Mining only
Oropharyngeal Neoplasms	Oropharyngeal neoplasm	Pubtator	26334652	Associate	★☆☆☆☆ Found in Text Mining only
ovarian neoplasm	Ovarian neoplasm	BEFREE	30221688		★☆☆☆☆ Found in Text Mining only
Peripheral motor neuropathy	Motor nerve neuritis	BEFREE	16685654		★☆☆☆☆ Found in Text Mining only
Peripheral Nervous System Diseases	Nervous System Diseases	HPO_DG			★☆☆☆☆ Found in Text Mining only
Peroxisomal Disorders	Peroxisomal disorder	Pubtator	2085845	Inhibit	★☆☆☆☆ Found in Text Mining only
Pituitary Adenoma	Pituitary adenoma	BEFREE	31519191		★☆☆☆☆ Found in Text Mining only
Polyneuropathy	Polyneuropathy	CTD_human_DG	16685654		★☆☆☆☆ Found in Text Mining only
Polyneuropathy, Critical Illness	Polyneuropathy	CTD_human_DG	16685654		★☆☆☆☆ Found in Text Mining only
Polyneuropathy, Familial	Polyneuropathy	CTD_human_DG	16685654		★☆☆☆☆ Found in Text Mining only
Polyneuropathy, Motor	Polyneuropathy	CTD_human_DG	16685654		★☆☆☆☆ Found in Text Mining only
Primary hypogonadism	Hypogonadism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Refsum Disease	Refsum Disease	BEFREE	11948235		★☆☆☆☆ Found in Text Mining only
Small vessel vasculitis	Small vessel vasculitis	BEFREE	27863214, 29599785		★☆☆☆☆ Found in Text Mining only
Squamous Cell Carcinoma of Head and Neck	Squamous cell carcinoma	Pubtator	17079134, 36142875	Associate	★☆☆☆☆ Found in Text Mining only
Testicular Diseases	Testicular disease	Pubtator	35996156	Associate	★☆☆☆☆ Found in Text Mining only
Uterine Cervical Neoplasms	Uterine neoplasm	Pubtator	23405241	Associate	★☆☆☆☆ Found in Text Mining only
Vasculitis	Vasculitis	BEFREE	30253046		★☆☆☆☆ Found in Text Mining only