SYCE2

Summary

SYCE2 (synaptonemal complex central element protein 2, HGNC:27411) is a protein-coding gene on chromosome 19p13.13, encoding Synaptonemal complex central element protein 2 (Q6PIF2). Major component of the transverse central element of synaptonemal complexes (SCS), formed between homologous chromosomes during meiotic prophase.

The protein encoded by this gene is part of the synaptonemal complex formed between homologous chromosomes during meiotic prophase. The encoded protein associates with SYCP1 and SYCE1 and is found only where chromosome cores are synapsed.

Source: NCBI Gene 256126 — RefSeq curated summary.

At a glance

• GWAS associations: 8
• Clinical variants (ClinVar): 41 total — 1 pathogenic
• MANE Select transcript: NM_001105578

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27411
Approved symbol	SYCE2
Name	synaptonemal complex central element protein 2
Location	19p13.13
Locus type	gene with protein product
Status	Approved
Aliases	CESC1
Ensembl gene	ENSG00000161860
Ensembl biotype	protein_coding
OMIM	611487
Entrez	256126

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 5 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000293695, ENST00000591229, ENST00000592819, ENST00000939778, ENST00000939779, ENST00000939780

RefSeq mRNA: 1 — MANE Select: NM_001105578 NM_001105578

CCDS: CCDS42509

Canonical transcript exons

ENST00000293695 — 6 exons

Exon	Start	End
ENSE00001128592	12900460	12900648
ENSE00001260506	12898786	12899385
ENSE00001260525	12900004	12900120
ENSE00001260528	12904492	12904666
ENSE00001313453	12918222	12918337
ENSE00001723803	12919243	12919293

Expression profiles

Bgee: expression breadth ubiquitous, 160 present calls, max score 89.53.

FANTOM5 (CAGE): breadth broad, TPM avg 0.5413 / max 49.6193, expressed in 262 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
179421	0.4594	242
179420	0.0292	9
179418	0.0284	7
179419	0.0243	4

Top tissues by expression

256 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	89.53	gold quality
left testis	UBERON:0004533	89.17	gold quality
testis	UBERON:0000473	87.29	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.79	gold quality
right lobe of liver	UBERON:0001114	79.66	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	76.33	gold quality
cerebellar hemisphere	UBERON:0002245	75.75	gold quality
cerebellar cortex	UBERON:0002129	75.54	gold quality
right hemisphere of cerebellum	UBERON:0014890	75.08	gold quality
lower esophagus mucosa	UBERON:0035834	74.56	gold quality
ventricular zone	UBERON:0003053	74.27	gold quality
left ovary	UBERON:0002119	73.86	gold quality
tibial nerve	UBERON:0001323	73.67	gold quality
ganglionic eminence	UBERON:0004023	73.19	gold quality
cerebellum	UBERON:0002037	73.16	gold quality
right ovary	UBERON:0002118	72.70	gold quality
mucosa of stomach	UBERON:0001199	71.74	gold quality
popliteal artery	UBERON:0002250	71.71	gold quality
tibial artery	UBERON:0007610	71.67	gold quality
adult organism	UBERON:0007023	71.47	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	70.92	gold quality
lower esophagus muscularis layer	UBERON:0035833	70.90	gold quality
lower esophagus	UBERON:0013473	70.88	gold quality
muscle layer of sigmoid colon	UBERON:0035805	70.47	gold quality
ovary	UBERON:0000992	70.19	gold quality
aorta	UBERON:0000947	69.97	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	69.95	gold quality
amygdala	UBERON:0001876	69.73	gold quality
body of stomach	UBERON:0001161	69.70	gold quality
right lobe of thyroid gland	UBERON:0001119	69.40	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	2.22

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

31 targeting SYCE2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-551B-5P	99.96	71.28	3493
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-221-3P	99.86	71.56	1329
HSA-MIR-222-3P	99.86	71.35	1337
HSA-MIR-3151-5P	99.86	63.83	1069
HSA-MIR-3150A-3P	99.76	64.44	1640
HSA-MIR-6763-5P	99.76	64.68	1767
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-3175	99.65	66.30	2031
HSA-MIR-3136-3P	99.57	66.59	781
HSA-MIR-7155-3P	99.57	66.48	794
HSA-MIR-1207-5P	99.49	69.11	2983
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-6839-3P	99.39	68.86	1301
HSA-MIR-4727-5P	99.23	67.55	1154
HSA-MIR-4291	99.20	68.88	2969
HSA-MIR-491-5P	99.13	65.98	1468
HSA-MIR-4254	99.11	65.15	1315
HSA-MIR-4763-3P	99.10	67.83	2649
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-6738-3P	99.03	67.14	1326
HSA-MIR-939-3P	98.97	65.07	2347
HSA-MIR-5001-3P	98.91	67.28	1394
HSA-MIR-887-5P	98.82	65.90	1347
HSA-MIR-663B	97.40	62.91	664
HSA-MIR-939-5P	97.10	65.80	1579
HSA-MIR-3139	96.68	66.77	652
HSA-MIR-1343-5P	96.48	66.06	1506
HSA-MIR-28-5P	96.16	66.12	579

Literature-anchored findings (GeneRIF, showing 2)

• a model of chromosome synapsis driven by growth of SYCE2-TEX12 higher-order structures within the CE of the SC. (PMID:22870393)
• Structural basis of meiotic chromosome synaptic elongation through hierarchical fibrous assembly of SYCE2-TEX12. (PMID:34373646)

Cross-species orthologs

1 orthologs

Organism	Symbol	Gene ID
mus_musculus	Syce2	ENSMUSG00000003824

Protein

Protein identifiers

Synaptonemal complex central element protein 2 — Q6PIF2 (reviewed: Q6PIF2)

Alternative names: Central element synaptonemal complex protein 1

All UniProt accessions (2): K7EM50, Q6PIF2

UniProt curated annotations — full annotation on UniProt →

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 synaptonemal complex assembly, stabilization and recombination.

Subunit / interactions. Homodimer. Found in a complex with SYCP1 and SYCE1. Interacts with SYCP1, SYCE1 and SYCE3. Interacts with TEX12.

Subcellular location. Nucleus. Chromosome.

Similarity. Belongs to the SYCE family.

RefSeq proteins (1): NP_001099048* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR034609	Syce2	Family

UniProt features (7 total): region of interest 2, compositionally biased region 2, chain 1, coiled-coil region 1, helix 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
6R17	X-RAY DIFFRACTION	2.42
6YQF	X-RAY DIFFRACTION	3.33

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6PIF2-F1	73.60	0.48

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-1221632	Meiotic synapsis
R-HSA-1474165	Reproduction
R-HSA-1500620	Meiosis
R-HSA-1640170	Cell Cycle

MSigDB gene sets: 168 (showing top): GSE45365_NK_CELL_VS_BCELL_DN, GOBP_MEIOTIC_CHROMOSOME_SEGREGATION, GOBP_CHROMOSOME_ORGANIZATION, REACTOME_MEIOTIC_SYNAPSIS, KONG_E2F3_TARGETS, GOLDRATH_ANTIGEN_RESPONSE, GOBP_SYNAPTONEMAL_COMPLEX_ORGANIZATION, GOBP_ORGANELLE_FISSION, GOBP_CHROMOSOME_ORGANIZATION_INVOLVED_IN_MEIOTIC_CELL_CYCLE, SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP, GOBP_HOMOLOGOUS_CHROMOSOME_SEGREGATION, GOBP_MEIOTIC_CELL_CYCLE_PROCESS, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, CUI_TCF21_TARGETS_2_UP, GOBP_HOMOLOGOUS_CHROMOSOME_PAIRING_AT_MEIOSIS

GO Biological Process (3): synaptonemal complex assembly (GO:0007130), cell division (GO:0051301), meiotic cell cycle (GO:0051321)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (4): central element (GO:0000801), nucleoplasm (GO:0005654), chromosome (GO:0005694), nucleus (GO:0005634)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Meiosis	1
Reproduction	1
Cell Cycle	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
homologous chromosome pairing at meiosis	1
cellular component assembly	1
chromosome organization involved in meiotic cell cycle	1
synaptonemal complex organization	1
cellular process	1
cell cycle	1
sexual reproduction	1
reproductive process	1
meiotic nuclear division	1
binding	1
synaptonemal complex	1
nuclear lumen	1
intracellular membraneless organelle	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

602 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SYCE2	SYCE1	Q8N0S2	999
SYCE2	TEX12	Q9BXU0	997
SYCE2	SYCP1	Q15431	996
SYCE2	SYCE3	A1L190	983
SYCE2	SYCP3	Q8IZU3	944
SYCE2	C14orf39	Q8N1H7	886
SYCE2	DAZL	Q92904	871
SYCE2	SYCP2	Q9BX26	817
SYCE2	HORMAD1	Q86X24	788
SYCE2	SPO11	Q9Y5K1	742
SYCE2	STAG3	Q9UJ98	710
SYCE2	HORMAD2	Q8N7B1	707
SYCE2	SMC1B	Q8NDV3	635
SYCE2	REC8	O95072	628
SYCE2	RAD21L1	Q9H4I0	616

IntAct

54 interactions, top by confidence:

A	B	Type	Score
KRT31	HGS	psi-mi:“MI:0914”(association)	0.780
SYCE2	MED4	psi-mi:“MI:0915”(physical association)	0.670
SYCE2	TRIM69	psi-mi:“MI:0915”(physical association)	0.560
CDC37	SYCE2	psi-mi:“MI:0915”(physical association)	0.560
SYCE2	HOMER1	psi-mi:“MI:0915”(physical association)	0.560
SYCE2	KIFC3	psi-mi:“MI:0915”(physical association)	0.560
CCDC196	SYCE2	psi-mi:“MI:0915”(physical association)	0.560
SYCE2	TEX12	psi-mi:“MI:0915”(physical association)	0.560
SYCE2	TRIML2	psi-mi:“MI:0915”(physical association)	0.560
SYCE2	NAP1L5	psi-mi:“MI:0915”(physical association)	0.560
GAD2	SYCE2	psi-mi:“MI:0915”(physical association)	0.560
SYCE2	IFT20	psi-mi:“MI:0915”(physical association)	0.560
SYCE2	TSNAX	psi-mi:“MI:0915”(physical association)	0.560
SYCE2	MED11	psi-mi:“MI:0915”(physical association)	0.560
SYCE2	TRIM27	psi-mi:“MI:0914”(association)	0.350
WFDC8	ACTA2	psi-mi:“MI:0914”(association)	0.350
SYCE2	TRIM69	psi-mi:“MI:0915”(physical association)	0.000
CDC37	SYCE2	psi-mi:“MI:0915”(physical association)	0.000
SYCE2	MED4	psi-mi:“MI:0915”(physical association)	0.000
SYCE2	TEX12	psi-mi:“MI:0915”(physical association)	0.000
HOMER1	SYCE2	psi-mi:“MI:0915”(physical association)	0.000
KIFC3	SYCE2	psi-mi:“MI:0915”(physical association)	0.000
CCDC196	SYCE2	psi-mi:“MI:0915”(physical association)	0.000
SYCE2	TRIML2	psi-mi:“MI:0915”(physical association)	0.000
SYCE2	CCDC196	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (21): SYCE2 (Two-hybrid), SYCE2 (Two-hybrid), SYCE2 (Two-hybrid), SYCE2 (Two-hybrid), SYCE2 (Two-hybrid), SYCE2 (Two-hybrid), SYCE2 (Two-hybrid), SYCE2 (Two-hybrid), MED11 (Two-hybrid), NAP1L5 (Two-hybrid), TRIML2 (Two-hybrid), TRIM69 (Two-hybrid), LINC00238 (Two-hybrid), SYCE2 (Affinity Capture-Western), SYCE2 (Affinity Capture-RNA)

ESM2 similar proteins: A0JNG4, A1L4K1, A6QQX5, G3X8Y1, H0UZ81, I1VZH0, O95361, P18302, P97432, Q15554, Q38HM4, Q3UFB2, Q3V3A7, Q501R9, Q505B8, Q58D15, Q5EAN7, Q5PQN5, Q5R760, Q5R846, Q5RC94, Q5REJ9, Q5RF77, Q5T7N3, Q5XIH6, Q60953, Q62881, Q6P752, Q6PIF2, Q6QA27, Q6ZRF8, Q810L3, Q8BSI6, Q8BYU6, Q8BZ52, Q8N9B5, Q91VL8, Q91Z63, Q969Q1, Q96DX7

Diamond homologs: Q505B8, Q6PIF2

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
SYCE2	“form complex”	Synaptonemal_complex	binding

Disease & clinical

Clinical variants and AI predictions

ClinVar

41 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	29
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
193976	NM_000159.4(GCDH):c.1244-2A>C	Pathogenic

SpliceAI

984 predictions. Top by Δscore:

Variant	Effect	Δscore
19:12900454:TCATA:T	donor_loss	1.0000
19:12900455:CATA:C	donor_loss	1.0000
19:12900457:TACCT:T	donor_loss	1.0000
19:12900458:A:AT	donor_loss	1.0000
19:12900646:AAC:A	acceptor_gain	1.0000
19:12900649:C:CC	acceptor_gain	1.0000
19:12900649:CT:C	acceptor_loss	1.0000
19:12900650:T:G	acceptor_loss	1.0000
19:12918215:T:TA	donor_gain	1.0000
19:12918216:CCTCA:C	donor_loss	1.0000
19:12918217:CTCAC:C	donor_loss	1.0000
19:12918218:TCACC:T	donor_loss	1.0000
19:12918219:CACCT:C	donor_loss	1.0000
19:12918220:ACCTA:A	donor_loss	1.0000
19:12918221:C:CT	donor_loss	1.0000
19:12918221:CCTAG:C	donor_gain	1.0000
19:12918225:G:C	donor_gain	1.0000
19:12918243:T:TA	donor_gain	1.0000
19:12900456:ATAC:A	donor_gain	0.9900
19:12900645:AAAC:A	acceptor_gain	0.9900
19:12900647:AC:A	acceptor_gain	0.9900
19:12900648:CC:C	acceptor_gain	0.9900
19:12900652:T:TC	acceptor_gain	0.9900
19:12918220:A:AC	donor_gain	0.9900
19:12918221:C:CC	donor_gain	0.9900
19:12919241:A:AC	donor_gain	0.9900
19:12919241:ACTC:A	donor_gain	0.9900
19:12919242:C:CC	donor_gain	0.9900
19:12919242:CTCC:C	donor_gain	0.9900
19:12919244:C:CA	donor_gain	0.9900

AlphaMissense

1440 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:12900518:A:G	L146P	0.988
19:12904544:C:G	R85P	0.983
19:12900638:A:G	L106P	0.977
19:12904568:A:G	L77P	0.977
19:12904502:A:G	L99P	0.976
19:12900569:A:G	L129P	0.969
19:12900560:A:G	F132S	0.963
19:12900518:A:T	L146H	0.959
19:12904578:C:G	A74P	0.954
19:12904536:C:G	D88H	0.951
19:12900559:G:C	F132L	0.945
19:12900559:G:T	F132L	0.945
19:12900561:A:G	F132L	0.945
19:12904514:A:G	F95S	0.943
19:12904535:T:A	D88V	0.940
19:12904534:G:C	D88E	0.937
19:12904534:G:T	D88E	0.937
19:12904535:T:G	D88A	0.937
19:12904545:G:C	R85G	0.932
19:12904513:G:C	F95L	0.931
19:12904513:G:T	F95L	0.931
19:12904515:A:G	F95L	0.931
19:12904523:A:G	M92T	0.931
19:12904577:G:T	A74D	0.926
19:12900539:A:G	I139T	0.914
19:12904526:A:G	L91P	0.912
19:12900518:A:C	L146R	0.910
19:12904589:A:G	L70P	0.910
19:12904535:T:C	D88G	0.908
19:12900581:A:G	I125T	0.904

dbSNP variants (sampled 300 via entrez): RS1000077135 (19:12914291 G>A), RS1000078106 (19:12906218 G>A), RS1000368852 (19:12902594 C>G,T), RS1000554394 (19:12914524 C>A,G,T), RS1000585927 (19:12917117 T>A,C), RS1000643479 (19:12919113 T>A,C,G), RS1000682405 (19:12905064 TGA>T), RS1000793896 (19:12902815 A>G,T), RS1000813360 (19:12910753 C>G,T), RS1000956527 (19:12917461 C>A), RS1001073929 (19:12899198 G>A,C), RS1001151272 (19:12913334 T>C), RS1001269918 (19:12911920 G>A), RS1001282291 (19:12921157 A>G), RS1001487487 (19:12913153 G>A)

Disease associations

OMIM: gene MIM:611487 | disease phenotypes: MIM:231670

GenCC curated gene-disease

Mondo (1): glutaryl-CoA dehydrogenase deficiency (MONDO:0009281)

Orphanet (1): Glutaryl-CoA dehydrogenase deficiency (Orphanet:25)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

8 associations (top):

Study	Trait	p-value
GCST001765_24	Red blood cell traits	8.000000e-20
GCST002595_9	Clozapine-induced agranulocytosis	1.000000e-06
GCST90002385_497	High light scatter reticulocyte count	2.000000e-14
GCST90002386_68	High light scatter reticulocyte percentage of red cells	2.000000e-23
GCST90002391_106	Mean corpuscular hemoglobin concentration	7.000000e-13
GCST90002400_268	Plateletcrit	7.000000e-13
GCST90002402_617	Platelet count	1.000000e-09
GCST90002404_564	Red cell distribution width	1.000000e-41

EFO canonical traits (6, from GWAS)

EFO ID	Trait name
EFO:0004527	mean corpuscular hemoglobin
EFO:0007986	reticulocyte count
EFO:0004528	mean corpuscular hemoglobin concentration
EFO:0007985	platelet crit
EFO:0004309	platelet count
EFO:0009188	Red cell distribution width

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C536833	Glutaric Acidemia I (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	4
Benzo(a)pyrene	increases expression, increases methylation	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
methylmercuric chloride	decreases expression	1
decabromobiphenyl ether	affects expression	1
ethyl-p-hydroxybenzoate	decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
potassium chromate(VI)	affects cotreatment, increases expression	1
2,3-bis(3’-hydroxybenzyl)butyrolactone	affects cotreatment, increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
epigallocatechin gallate	affects cotreatment, increases expression	1
di-n-butylphosphoric acid	affects expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Arsenic	affects methylation	1
Coumestrol	affects cotreatment, increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Dimethyl Sulfoxide	affects expression	1
Ethyl Methanesulfonate	increases expression	1
Lipopolysaccharides	decreases expression, affects response to substance, increases expression	1
Methyl Methanesulfonate	increases expression	1
Quercetin	increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cyclosporine	increases expression	1

Clinical trials (associated diseases)

3 trials via MONDO — disease-level, not drug-specific.

Trial	Phase	Status	Title
NCT06217861	PHASE1	RECRUITING	A Study to Evaluate the Tolerability, Safety and Efficacy of VGM-R02b
NCT03655223	Not specified	ENROLLING_BY_INVITATION	Early Check: Expanded Screening in Newborns
NCT05910151	Not specified	UNKNOWN	Selective Screening of Children for Hereditary Metabolic Diseases by Tandem Mass Spectrometry in Kazakhstan