SYCE1L

Summary

SYCE1L (synaptonemal complex central element protein 1 like, HGNC:37236) is a protein-coding gene on chromosome 16q23.1, encoding Synaptonemal complex central element protein 1-like (A8MT33). May be involved in meiosis.

Predicted to be involved in synaptonemal complex assembly. Located in intermediate filament cytoskeleton.

Source: NCBI Gene 100130958 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 61 total — 1 pathogenic
• MANE Select transcript: NM_001129979

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:37236
Approved symbol	SYCE1L
Name	synaptonemal complex central element protein 1 like
Location	16q23.1
Locus type	gene with protein product
Status	Approved
Aliases	MRP2
Ensembl gene	ENSG00000205078
Ensembl biotype	protein_coding
OMIM	619954
Entrez	100130958

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000378644, ENST00000563157, ENST00000568925

RefSeq mRNA: 2 — MANE Select: NM_001129979 NM_001129979, NM_001348924

CCDS: CCDS45533

Canonical transcript exons

ENST00000378644 — 11 exons

Exon	Start	End
ENSE00001478209	77212857	77213215
ENSE00001478210	77212574	77212646
ENSE00001478211	77212282	77212369
ENSE00001531643	77211213	77211276
ENSE00001531648	77212130	77212199
ENSE00001531655	77208210	77208269
ENSE00001636027	77206441	77206500
ENSE00001639574	77208465	77208539
ENSE00001788312	77199408	77199512
ENSE00002450002	77209097	77209144
ENSE00002511376	77209417	77209471

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 96.16.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.5039 / max 99.2598, expressed in 1300 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
155066	1.8611	811
155065	1.5675	729
155064	1.3691	554
155067	0.6786	391
155063	0.0276	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	96.16	gold quality
right testis	UBERON:0004534	88.80	gold quality
left testis	UBERON:0004533	88.57	gold quality
testis	UBERON:0000473	87.63	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	87.09	gold quality
bone marrow cell	CL:0002092	84.26	gold quality
prostate gland	UBERON:0002367	84.01	gold quality
uterine cervix	UBERON:0000002	83.68	gold quality
endocervix	UBERON:0000458	81.30	gold quality
left ovary	UBERON:0002119	81.01	gold quality
left uterine tube	UBERON:0001303	80.92	gold quality
right ovary	UBERON:0002118	80.64	gold quality
ovary	UBERON:0000992	80.37	gold quality
ectocervix	UBERON:0012249	80.23	gold quality
thoracic mammary gland	UBERON:0005200	79.64	gold quality
hindlimb stylopod muscle	UBERON:0004252	79.24	gold quality
mucosa of transverse colon	UBERON:0004991	79.20	gold quality
metanephros cortex	UBERON:0010533	79.00	gold quality
right hemisphere of cerebellum	UBERON:0014890	78.95	gold quality
cerebellar hemisphere	UBERON:0002245	78.59	gold quality
cerebellum	UBERON:0002037	78.58	gold quality
cerebellar cortex	UBERON:0002129	78.58	gold quality
left lobe of thyroid gland	UBERON:0001120	78.50	gold quality
cortex of kidney	UBERON:0001225	78.42	gold quality
body of uterus	UBERON:0009853	78.30	gold quality
minor salivary gland	UBERON:0001830	77.98	gold quality
thyroid gland	UBERON:0002046	77.81	gold quality
right lobe of thyroid gland	UBERON:0001119	77.75	gold quality
saliva-secreting gland	UBERON:0001044	77.74	gold quality
right uterine tube	UBERON:0001302	77.28	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-GEOD-125970	yes	20.08
E-ANND-3	yes	4.49
E-MTAB-7316	no	404.96

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-199g17.9	ENSDARG00000076609
mus_musculus	Syce1l	ENSMUSG00000033409
rattus_norvegicus	Syce1l	ENSRNOG00000075594

Paralogs (1): SYCE1 (ENSG00000171772)

Protein

Protein identifiers

Synaptonemal complex central element protein 1-like — A8MT33 (reviewed: A8MT33)

Alternative names: Meiosis-related protein

All UniProt accessions (2): A8MT33, H3BME6

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in meiosis.

Similarity. Belongs to the SYCE family.

RefSeq proteins (2): NP_001123451, NP_001335853 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026676	SYCE1	Family

Pfam: PF15233

UniProt features (4 total): region of interest 2, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A8MT33-F1	80.56	0.57

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 52 (showing top): GOBP_MEIOTIC_CHROMOSOME_SEGREGATION, GOBP_CHROMOSOME_ORGANIZATION, GOBP_SYNAPTONEMAL_COMPLEX_ORGANIZATION, GOBP_ORGANELLE_FISSION, GOBP_CHROMOSOME_ORGANIZATION_INVOLVED_IN_MEIOTIC_CELL_CYCLE, GOBP_HOMOLOGOUS_CHROMOSOME_SEGREGATION, GOBP_MEIOTIC_CELL_CYCLE_PROCESS, GOBP_HOMOLOGOUS_CHROMOSOME_PAIRING_AT_MEIOSIS, GOBP_NUCLEAR_CHROMOSOME_SEGREGATION, GOBP_MEIOTIC_CELL_CYCLE, GOBP_CELL_CYCLE_PROCESS, GOCC_NUCLEAR_CHROMOSOME, GOCC_CONDENSED_NUCLEAR_CHROMOSOME, GOBP_CHROMOSOME_SEGREGATION, GOBP_MEIOSIS_I_CELL_CYCLE_PROCESS

GO Biological Process (3): synaptonemal complex assembly (GO:0007130), meiotic cell cycle (GO:0051321), synaptonemal complex organization (GO:0070193)

GO Molecular Function (0):

GO Cellular Component (2): synaptonemal complex (GO:0000795), intermediate filament cytoskeleton (GO:0045111)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
homologous chromosome pairing at meiosis	1
cellular component assembly	1
chromosome organization involved in meiotic cell cycle	1
synaptonemal complex organization	1
cell cycle	1
sexual reproduction	1
reproductive process	1
meiotic nuclear division	1
chromosome organization	1
synaptonemal structure	1
cytoskeleton	1

Protein interactions and networks

STRING

258 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SYCE1L	SYCE2	Q6PIF2	512
SYCE1L	VAT1L	Q9HCJ6	499
SYCE1L	ZNF567	Q8N184	490
SYCE1L	MON1B	Q7L1V2	480
SYCE1L	ZNF775	Q96BV0	450
SYCE1L	URB2	Q14146	426
SYCE1L	RAD21	O60216	417
SYCE1L	B8ZZ87	B8ZZ87	417
SYCE1L	DENND2C	Q68D51	412
SYCE1L	OSBPL7	Q9BZF2	400
SYCE1L	ZNF710	Q8N1W2	377
SYCE1L	HUS1B	Q8NHY5	376
SYCE1L	ZNF593	O00488	370
SYCE1L	SLC35E2A	P0CK97	369
SYCE1L	CTTNBP2NL	Q9P2B4	368

IntAct

0 interactions, top by confidence:

BioGRID (38): SYCE1L (Synthetic Lethality), SYCE1L (Two-hybrid), SYCE1L (Two-hybrid), SYCE1L (Two-hybrid), SYCE1L (Two-hybrid), SYCE1L (Two-hybrid), SYCE1L (Two-hybrid), SYCE1L (Two-hybrid), SYCE1L (Two-hybrid), SYCE1L (Two-hybrid), SYCE1L (Two-hybrid), SYCE1L (Two-hybrid), SYCE1L (Two-hybrid), SYCE1L (Two-hybrid), SYCE1L (Two-hybrid)

ESM2 similar proteins: A0A494C1R9, A2AKB4, A2APT9, A6NKD2, A8MT33, B0BN44, E9PGG2, F5GYI3, O19110, O88852, P0CV98, P0CV99, P0CW00, P0CW01, Q01534, Q03386, Q0P5N2, Q12967, Q14684, Q2M329, Q3U3N0, Q5F267, Q5I0E2, Q5R5G8, Q5R866, Q5SYB0, Q5VTJ3, Q60953, Q69ZB3, Q6ZUX3, Q7TQI8, Q80VJ8, Q80VR2, Q86VY4, Q8BSI6, Q8IZJ4, Q8N831, Q8VD63, Q95LS7, Q96FG2

Diamond homologs: A8MT33, Q32LK9, Q4R7J8, Q5D525, Q5XHZ2, Q8N0S2, Q9D495

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	50
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
564342	GRCh37/hg19 16q22.2-24.3(chr16:72515938-90155062)x3	Pathogenic

SpliceAI

2111 predictions. Top by Δscore:

Variant	Effect	Δscore
16:77199503:G:GT	donor_gain	1.0000
16:77208209:G:C	acceptor_gain	1.0000
16:77208457:T:TA	acceptor_gain	1.0000
16:77211196:T:TA	acceptor_gain	1.0000
16:77211197:G:A	acceptor_gain	1.0000
16:77212195:GGAGA:G	donor_gain	1.0000
16:77212196:GAGA:G	donor_gain	1.0000
16:77212196:GAGAG:G	donor_gain	1.0000
16:77212197:A:T	donor_gain	1.0000
16:77212198:GA:G	donor_gain	1.0000
16:77212200:G:GG	donor_gain	1.0000
16:77199511:AGG:A	donor_loss	0.9900
16:77199513:GTA:G	donor_gain	0.9900
16:77206538:TTTC:T	donor_gain	0.9900
16:77206593:A:T	donor_gain	0.9900
16:77208205:TTCAG:T	acceptor_gain	0.9900
16:77208206:TCAG:T	acceptor_gain	0.9900
16:77208207:CAG:C	acceptor_gain	0.9900
16:77208208:A:AG	acceptor_gain	0.9900
16:77208208:AGA:A	acceptor_gain	0.9900
16:77208208:AGAG:A	acceptor_gain	0.9900
16:77208209:G:GG	acceptor_gain	0.9900
16:77208209:GA:G	acceptor_gain	0.9900
16:77208209:GAGG:G	acceptor_gain	0.9900
16:77209416:GA:G	acceptor_gain	0.9900
16:77209468:AGAG:A	donor_loss	0.9900
16:77209469:GAG:G	donor_gain	0.9900
16:77209469:GAGG:G	donor_loss	0.9900
16:77209473:T:G	donor_loss	0.9900
16:77211277:G:GG	donor_gain	0.9900

AlphaMissense

1574 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
16:77208240:T:C	L51P	0.982
16:77208249:G:C	R54P	0.971
16:77208261:T:C	L58P	0.963
16:77206492:T:C	L38P	0.958
16:77208252:T:C	I55T	0.947
16:77208269:G:C	A61P	0.931
16:77208252:T:G	I55S	0.915
16:77211271:T:C	F140L	0.902
16:77211273:C:A	F140L	0.902
16:77211273:C:G	F140L	0.902
16:77206483:T:A	V35E	0.898
16:77209140:G:C	K100N	0.895
16:77209140:G:T	K100N	0.895
16:77211267:G:C	W138C	0.888
16:77211267:G:T	W138C	0.888
16:77206471:T:C	L31S	0.885
16:77208240:T:A	L51Q	0.881
16:77208519:T:C	L79P	0.880
16:77209118:T:C	L93P	0.878
16:77212143:G:C	R146P	0.875
16:77209419:G:C	A103P	0.874
16:77208243:T:G	I52S	0.869
16:77209423:T:C	L104P	0.858
16:77208240:T:G	L51R	0.845
16:77212158:T:C	I151T	0.842
16:77212155:A:T	E150V	0.841
16:77208243:T:C	I52T	0.840
16:77208212:G:A	G42R	0.837
16:77208212:G:C	G42R	0.837
16:77212146:T:C	L147P	0.835

dbSNP variants (sampled 300 via entrez): RS1000183280 (16:77201838 G>A), RS1000222090 (16:77210997 C>A), RS1000393159 (16:77197799 G>T), RS1000427595 (16:77202126 G>A), RS1000516510 (16:77213316 A>T), RS1000526196 (16:77200631 C>G), RS1000654199 (16:77207051 T>C), RS1000720290 (16:77211875 C>G), RS1000723007 (16:77206762 C>A), RS1000723677 (16:77200422 A>C), RS1000767676 (16:77197590 A>G), RS1001112626 (16:77205069 A>G,T), RS1001121038 (16:77199112 G>T), RS1001190618 (16:77202993 T>C), RS1001345900 (16:77203199 T>C)

Disease associations

OMIM: gene MIM:619954 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

Study	Trait	p-value
GCST002411_7	Colorectal cancer	5.000000e-11
GCST004125_24	Type 2 diabetes (age of onset)	6.000000e-06
GCST007001_10	Cerebrospinal AB1-42 levels in normal cognition	2.000000e-07

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004670	beta-amyloid 1-42 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

13 total (human), top 13 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases methylation	2
triphenyl phosphate	affects expression	1
bisphenol A	decreases methylation	1
ICG 001	decreases expression	1
jinfukang	affects cotreatment, increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Rotenone	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cyclosporine	decreases expression	1
Aflatoxin B1	increases methylation	1
Particulate Matter	decreases expression, increases abundance	1

Clinical trials (associated diseases)

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