SYCN

Summary

SYCN (syncollin, HGNC:18442) is a protein-coding gene on chromosome 19q13.2, encoding Syncollin (Q0VAF6). Functions in exocytosis in pancreatic acinar cells regulating the fusion of zymogen granules with each other.

Predicted to be involved in exocytosis. Predicted to be located in zymogen granule membrane.

Source: NCBI Gene 342898 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 33 total
• MANE Select transcript: NM_001080468

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18442
Approved symbol	SYCN
Name	syncollin
Location	19q13.2
Locus type	gene with protein product
Status	Approved
Aliases	SYL, FLJ27441
Ensembl gene	ENSG00000179751
Ensembl biotype	protein_coding
OMIM	620140
Entrez	342898

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000318438

RefSeq mRNA: 1 — MANE Select: NM_001080468 NM_001080468

CCDS: CCDS46070

Canonical transcript exons

ENST00000318438 — 2 exons

Exon	Start	End
ENSE00001238865	39203860	39204263
ENSE00001620914	39202825	39202996

Expression profiles

Bgee: expression breadth ubiquitous, 132 present calls, max score 99.87.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 29.0686 / max 39321.5342, expressed in 20 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
180844	29.0686	20

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
body of pancreas	UBERON:0001150	99.87	gold quality
pancreas	UBERON:0001264	94.21	gold quality
right testis	UBERON:0004534	87.21	gold quality
left testis	UBERON:0004533	86.87	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.71	gold quality
islet of Langerhans	UBERON:0000006	84.00	gold quality
testis	UBERON:0000473	83.73	gold quality
epithelial cell of pancreas	CL:0000083	81.59	silver quality
lower esophagus mucosa	UBERON:0035834	66.24	gold quality
right coronary artery	UBERON:0001625	65.75	gold quality
ectocervix	UBERON:0012249	65.34	gold quality
adult organism	UBERON:0007023	64.17	silver quality
body of stomach	UBERON:0001161	64.04	gold quality
fundus of stomach	UBERON:0001160	62.52	gold quality
right lobe of liver	UBERON:0001114	62.22	gold quality
left uterine tube	UBERON:0001303	61.58	gold quality
right adrenal gland	UBERON:0001233	60.93	gold quality
right uterine tube	UBERON:0001302	60.32	gold quality
esophagus mucosa	UBERON:0002469	60.00	gold quality
endocervix	UBERON:0000458	59.67	gold quality
metanephros cortex	UBERON:0010533	59.18	gold quality
oocyte	CL:0000023	58.21	gold quality
duodenum	UBERON:0002114	58.20	gold quality
amniotic fluid	UBERON:0000173	57.67	gold quality
stomach	UBERON:0000945	57.64	gold quality
left adrenal gland	UBERON:0001234	57.51	gold quality
uterine cervix	UBERON:0000002	57.31	gold quality
left adrenal gland cortex	UBERON:0035825	56.91	gold quality
right adrenal gland cortex	UBERON:0035827	56.43	gold quality
descending thoracic aorta	UBERON:0002345	56.30	gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 4.

Experiment	Marker?	Max mean expression
E-GEOD-81547	yes	5472.40
E-MTAB-5061	yes	18.83
E-ENAD-27	yes	7.31
E-GEOD-83139	no	2.57
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Additional serum biomarkers, particularly SYCN and REG1B, when combined with CA19.9, show promise as improved diagnostic indicators of pancreatic cancer, which therefore warrants further validation. (PMID:24007603)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	sycn.1	ENSDARG00000090469
danio_rerio	sycn.3	ENSDARG00000090899
danio_rerio	sycn.2	ENSDARG00000103687
mus_musculus	Sycn	ENSMUSG00000084174
rattus_norvegicus	Sycn	ENSRNOG00000019879

Protein

Protein identifiers

Syncollin — Q0VAF6 (reviewed: Q0VAF6)

Alternative names: Insulin synthesis-associated protein 1

All UniProt accessions (1): Q0VAF6

UniProt curated annotations — full annotation on UniProt →

Function. Functions in exocytosis in pancreatic acinar cells regulating the fusion of zymogen granules with each other. May have a pore-forming activity on membranes and regulate exocytosis in other exocrine tissues.

Subunit / interactions. Monomer and homooligomer; most probably hexameric. Interacts with GP2.

Subcellular location. Zymogen granule membrane. Zymogen granule lumen.

Post-translational modifications. Contains intrachain disulfide bonds.

RefSeq proteins (1): NP_001073937* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR028137	Syncollin	Family

Pfam: PF15138

UniProt features (3 total): signal peptide 1, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q0VAF6-F1	88.44	0.71

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-9925561	Developmental Lineage of Pancreatic Acinar Cells
R-HSA-1266738	Developmental Biology
R-HSA-9734767	Developmental Cell Lineages

MSigDB gene sets: 44 (showing top): GOCC_SECRETORY_GRANULE, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_EXOCYTOSIS, GOBP_SECRETION, GOCC_ZYMOGEN_GRANULE, GOCC_SECRETORY_VESICLE, GOCC_SECRETORY_GRANULE_MEMBRANE, RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP, YOSHIMURA_MAPK8_TARGETS_UP, FEVR_CTNNB1_TARGETS_UP, SERVITJA_ISLET_HNF1A_TARGETS_UP, GSE13522_WT_VS_IFNG_KO_SKING_T_CRUZI_Y_STRAIN_INF_DN, GSE13547_WT_VS_ZFX_KO_BCELL_ANTI_IGM_STIM_12H_UP, HES2_TARGET_GENES, MEF2D_TARGET_GENES

GO Biological Process (1): exocytosis (GO:0006887)

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

GO Cellular Component (4): zymogen granule membrane (GO:0042589), membrane (GO:0016020), secretory granule membrane (GO:0030667), cytoplasmic vesicle (GO:0031410)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Developmental Cell Lineages of the Exocrine Pancreas	1
Developmental Biology	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
vesicle-mediated transport	1
secretion by cell	1
vesicle fusion to plasma membrane	1
binding	1
secretory granule membrane	1
zymogen granule	1
cellular anatomical structure	1
secretory granule	1
cytoplasmic vesicle membrane	1
bounding membrane of organelle	1
cytoplasm	1
intracellular vesicle	1

Protein interactions and networks

STRING

468 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SYCN	ZG16	O60844	584
SYCN	PNLIPRP1	P54315	582
SYCN	REG1B	P48304	564
SYCN	RXFP4	Q8TDU9	523
SYCN	DTNA	Q9Y4J8	475
SYCN	GP2	P55259	472
SYCN	CELA3B	P08861	468
SYCN	CUZD1	Q86UP6	455
SYCN	CPA1	P15085	440
SYCN	FKRP	Q9H9S5	424
SYCN	PIGR	P01833	413
SYCN	CELA2A	P08217	413
SYCN	PTPRN2	Q92932	404
SYCN	WDR86	Q86TI4	381
SYCN	CLPSL1	A2RUU4	376

IntAct

4 interactions, top by confidence:

A	B	Type	Score
SYCN	AIP	psi-mi:“MI:0914”(association)	0.500
SYCN	AIP	psi-mi:“MI:0915”(physical association)	0.500
SYCN	H2BC9	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (7): HIST1H2BH (Proximity Label-MS), AIP (Affinity Capture-MS), CNTNAP1 (Affinity Capture-MS), SULF1 (Affinity Capture-MS), HSPA5 (Affinity Capture-MS), COL14A1 (Affinity Capture-MS), BIRC2 (Affinity Capture-MS)

ESM2 similar proteins: A0A346CIA0, A0A346CIB0, A0A346CIB2, A0A346CIB3, A0A7S8RFI7, A0S864, A0S865, A6MFK5, A7E3W2, A7X3V0, A7X4Q3, A7X4R0, A8HDK4, A8HDK7, A8HDK8, A8HDK9, B2BRQ6, F8J2B3, F8J2D7, F8J2E1, F8J2E2, F8J2E5, G3V686, O12961, O35775, O43278, O70513, O75339, P01384, P07358, P14612, P26776, P35495, P55314, P59899, P60615, P60616, P80915, P83880, P98136

Diamond homologs: O35775, Q0VAF6, Q8VCK7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	30
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

163 predictions. Top by Δscore:

Variant	Effect	Δscore
19:39203970:G:A	donor_gain	0.9000
19:39203736:C:CA	donor_gain	0.8500
19:39203884:TTGG:T	donor_gain	0.8000
19:39203918:C:CA	donor_gain	0.7900
19:39203862:G:A	donor_gain	0.7500
19:39202992:TGCAC:T	acceptor_loss	0.7300
19:39202993:GCAC:G	acceptor_loss	0.7300
19:39202994:CACCT:C	acceptor_loss	0.7300
19:39202995:AC:A	acceptor_loss	0.7300
19:39202996:CC:C	acceptor_loss	0.7300
19:39202997:C:T	acceptor_loss	0.7300
19:39202998:T:G	acceptor_loss	0.7300
19:39203002:A:C	acceptor_loss	0.7000
19:39202962:C:CC	acceptor_gain	0.6900
19:39202999:G:C	acceptor_loss	0.6900
19:39203000:AAA:A	acceptor_loss	0.6800
19:39203004:G:C	acceptor_loss	0.6800
19:39203001:AATG:A	acceptor_loss	0.6400
19:39203854:GGGCA:G	donor_loss	0.6400
19:39203855:GGCA:G	donor_loss	0.6400
19:39203856:GCA:G	donor_loss	0.6400
19:39203857:CA:C	donor_loss	0.6400
19:39203858:A:C	donor_loss	0.6400
19:39203859:C:CG	donor_loss	0.6400
19:39203860:C:G	donor_loss	0.6400
19:39203961:G:A	donor_gain	0.6300
19:39202961:GCTGC:G	acceptor_gain	0.6100
19:39203527:CAG:C	donor_gain	0.5900
19:39203895:T:TA	donor_gain	0.5900
19:39203861:T:C	donor_loss	0.5700

AlphaMissense

837 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:39203947:A:C	F103C	0.988
19:39203889:C:A	W122C	0.986
19:39203889:C:G	W122C	0.986
19:39203946:G:C	F103L	0.986
19:39203946:G:T	F103L	0.986
19:39203948:A:G	F103L	0.986
19:39203982:C:A	W91C	0.984
19:39203982:C:G	W91C	0.984
19:39203947:A:G	F103S	0.979
19:39204036:C:A	W73C	0.974
19:39204036:C:G	W73C	0.974
19:39203984:A:G	W91R	0.965
19:39203984:A:T	W91R	0.965
19:39203992:A:T	L88H	0.963
19:39204016:A:T	L80H	0.961
19:39203891:A:G	W122R	0.958
19:39203891:A:T	W122R	0.958
19:39203967:C:A	K96N	0.955
19:39203967:C:G	K96N	0.955
19:39203998:C:G	C86S	0.947
19:39203999:A:T	C86S	0.947
19:39204139:G:T	A39D	0.941
19:39203862:G:C	C131W	0.940
19:39204120:G:C	S45R	0.940
19:39204120:G:T	S45R	0.940
19:39204122:T:G	S45R	0.940
19:39203863:C:T	C131Y	0.931
19:39203998:C:T	C86Y	0.931
19:39204097:C:G	C53S	0.931
19:39204098:A:T	C53S	0.931

dbSNP variants (sampled 300 via entrez): RS1000168233 (19:39205970 G>A), RS1000471317 (19:39206032 T>C,G), RS1001572415 (19:39203134 G>T), RS1003338282 (19:39203816 G>A,T), RS1003564331 (19:39205523 A>G), RS1004244928 (19:39203060 A>G), RS1005222105 (19:39204316 A>G), RS1005617886 (19:39205052 G>A,T), RS1006807960 (19:39202366 C>A,G), RS1007377982 (19:39205670 A>C), RS1008796462 (19:39204832 G>A), RS1009261750 (19:39204448 T>G), RS1009670897 (19:39202569 C>A,T), RS1010323822 (19:39203563 A>G), RS1010504184 (19:39204419 G>A)

Disease associations

OMIM: gene MIM:620140 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	1
Oxygen	increases expression	1
Valproic Acid	increases methylation	1

Clinical trials (associated diseases)

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