BDgene

Core Gene from Gene Prioritization Pathways from PBA (Pathway-based Analysis) Enriched Pathways for Core Genes Enriched Pathways for Cross-disorder Genes

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Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

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Basic Info

Approved Symbol	SNAP25
Previous Symbol	SNAP
Symbol Alias	SNAP-25, RIC-4, RIC4, SEC9, bA416N4.2, dJ1068F16.2
Approved Name	synaptosomal-associated protein, 25kDa
Previous Name	synaptosomal-associated protein, 25kD
Name Alias	resistance to inhibitors of cholinesterase 4 homolog
Location	20p12-p11.2
Position	chr20:10218830-10307418, 1
External Links	HGNC: 11132 Entrez Gene: 6616 Ensembl: ENSG00000132639 UCSC: uc002wnr.2
No. of Studies	2 (Positive: 2; Negative: 0; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 2)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Hattori, E.,2009	SNP: rs1158497	After the two-stage analysis, markers in this gene remained nominally significant (allelic P<0.05) with the same allele being consistently over-represented in both the first and the follow-up stages.	Positive	Comment on Study
Etain, B., 2010	SNP: rs1051312, rs2076239, rs362987, rs363006, rs6039769, rs8636 Haplotype: rs2076239 - rs362987 - rs363006 - rs1051312(ACAC), rs362987 - rs363006 - rs1051312 - rs8636(CACC), rs6039769 - rs2076239 - rs362987 - rs363006(AAAG), SNAP25_promoter_SNP1 - rs6039769 - rs2076239 - rs362987(GAAA) Other variant: SNAP25_promoter_SNP1	one variant, located in the promoter region of SNAP25, was associated with early-onset BD but not with the late-onset subgroup. Individuals homozygous for this variant showed a significant higher SNAP25b expression level in prefrontal cortex.	Positive	Comment on Study

Gene functional annotation

Gene related GO terms (count: 32)

GO terms by PBA (count: 3)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0016020	membrane	cellular component	ISS	137
GO:0005886	plasma membrane	cellular component	TAS	360
GO:0007268	synaptic transmission	biological process	NAS[8760387]; TAS	116

GO terms by database search (count: 29)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005515	protein binding	molecular function	IPI[11438518]	563
GO:0007269	neurotransmitter secretion	biological process	TAS	15
GO:0016081	synaptic vesicle docking	biological process	NAS[8760387]	1
GO:0043005	neuron projection	cellular component	ISS	38
GO:0005829	cytosol	cellular component	TAS	223
GO:0001504	neurotransmitter uptake	biological process	NAS[8760387]	2
GO:0070032	synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex	cellular component	IBA	2
GO:0030054	cell junction	cellular component	IEA	88
GO:0048306	calcium-dependent protein binding	molecular function	ISS	7
GO:0014047	glutamate secretion	biological process	TAS	6
GO:0009405	pathogenesis	biological process	TAS	13
GO:0017075	syntaxin-1 binding	molecular function	IPI[12730201]	4
GO:0042734	presynaptic membrane	cellular component	TAS[15217342]	16
GO:0060291	long-term synaptic potentiation	biological process	IEA	14
GO:0031982	vesicle	cellular component	IDA[15459722]	20
GO:0048471	perinuclear region of cytoplasm	cellular component	IEA	50
GO:0010975	regulation of neuron projection development	biological process	IEA	4
GO:0005737	cytoplasm	cellular component	ISS	322
GO:0006112	energy reserve metabolic process	biological process	TAS	19
GO:0031083	BLOC-1 complex	cellular component	IDA[19546860]	3
GO:0005802	trans-Golgi network	cellular component	IEA	10
GO:0016082	synaptic vesicle priming	biological process	IBA	3
GO:0050796	regulation of insulin secretion	biological process	TAS[15537656]	24
GO:0031201	SNARE complex	cellular component	IDA[12130530]; ISS; TAS[15217342]	8
GO:0030426	growth cone	cellular component	ISS	22
GO:0044281	small molecule metabolic process	biological process	TAS	117
GO:0031629	synaptic vesicle fusion to presynaptic membrane	biological process	IBA	2
GO:0016079	synaptic vesicle exocytosis	biological process	TAS[15217342]	4
GO:0005484	SNAP receptor activity	molecular function	IBA	6

Gene related KEGG pathways (count: 1)

KEGG pathways by PBA (count: 0)

KEGG pathways by database search (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
hsa04130	SNARE interactions in vesicular transport	7

Gene related BioCarta pathways (count: 1)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
botulinPathway	Blockade of Neurotransmitter Relase by Botulinum Toxin	4

Gene related interactors from protein-protein interactions data in HPRD (count: 24)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
SNAP25	TRIM9	YES	in vitro;yeast 2-hybrid	11524423
SNAP25	STX12	YES	in vivo	10886332
SNAP25	PRKACA	NO	in vivo	12459461
SNAP25	ITSN1	NO	in vitro;in vivo;yeast 2-hybrid	10373452
SNAP25	KCNB1	NO	in vitro;in vivo	12403834
SNAP25	STX2	NO	in vivo	7768895
SNAP25	STX11	NO	yeast 2-hybrid	16169070 , 16189514
SNAP25	STXBP6	NO	in vitro;in vivo	12145319
SNAP25	CENPF	NO	in vivo;yeast 2-hybrid	16672379
SNAP25	RIMS1	NO	in vitro	11438521
SNAP25	STX1A	NO	in vitro;in vivo	7622514 , 9556632 , 11509230 , 7768895 , 10373452 , 10954418 , 17363971
SNAP25	SNAPIN	NO	in vitro;yeast 2-hybrid	10195194
SNAP25	STX4	NO	in vitro;yeast 2-hybrid	8760387 , 9168999
SNAP25	VAMP8	NO	in vitro	10336434
SNAP25	PRRT2	NO	yeast 2-hybrid	16169070
SNAP25	SYT9	NO	in vitro	12062043
SNAP25	HGS	NO	yeast 2-hybrid	10825299
SNAP25	SYT1	NO	in vitro	10692432
SNAP25	DNM1	NO	in vivo	10373452
SNAP25	STX3	NO	in vivo	7768895
SNAP25	PRKCA	NO	in vivo	12459461
SNAP25	ZDHHC17	NO	in vitro	15603740
SNAP25	SRCIN1	NO	in vitro;yeast 2-hybrid	10625663
SNAP25	SYT3	NO	in vitro	10692432

Related other genetic factors

Gene related SNPs (count: 43)

Literature-origin SNPs (count: 7)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs363006	chr20:10299435 - 10299435(1)	intron_variant; non_coding_transcript_variant	1(1/0/0)
rs8636	chr20:10307094 - 10307094(1)	3_prime_UTR_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs1158497	chr20:10237252 - 10237252(1)	intron_variant; non_coding_transcript_variant	1(1/0/0)
rs362987	chr20:10296804 - 10296804(1)	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs6039769	chr20:10218306 - 10218306(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(1/0/0)
rs1051312	chr20:10306440 - 10306440(1)	3_prime_UTR_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs2076239	chr20:10284532 - 10284532(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)

LD-proxies (count: 36)

rs_ID	Location	Functional Annotation
rs363004	chr20:10299149 - 10299149(1)	intron_variant; non_coding_transcript_variant
rs12480983	chr20:10298067 - 10298067(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs362991	chr20:10295633 - 10295633(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs362588	chr20:10290277 - 10290277(1)	intron_variant; non_coding_transcript_variant
rs362995	chr20:10296391 - 10296391(1)	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs6077722	chr20:10285440 - 10285440(1)	intron_variant; non_coding_transcript_variant
rs362998	chr20:10296973 - 10296973(1)	downstream_gene_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant
rs6077719	chr20:10281111 - 10281111(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs362999	chr20:10298312 - 10298312(1)	intron_variant; non_coding_transcript_variant
rs6077718	chr20:10280494 - 10280494(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs4510293	chr20:10277113 - 10277113(1)	intron_variant; non_coding_transcript_variant
rs6077712	chr20:10269640 - 10269640(1)	intron_variant; non_coding_transcript_variant
rs4813925	chr20:10305665 - 10305665(1)	intron_variant; non_coding_transcript_variant
rs3746544	chr20:10306436 - 10306436(1)	3_prime_UTR_variant; intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs362549	chr20:10289242 - 10289242(1)	intron_variant; non_coding_transcript_variant
rs2423487	chr20:10232447 - 10232447(1)	intron_variant; non_coding_transcript_variant
rs6108461	chr20:10286622 - 10286622(1)	intron_variant; non_coding_transcript_variant
rs1889189	chr20:10216438 - 10216438(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2225635	chr20:10225469 - 10225469(1)	intron_variant; non_coding_transcript_variant
rs6039807	chr20:10282928 - 10282928(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs6039806	chr20:10278006 - 10278006(1)	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs362574	chr20:10272434 - 10272434(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2327264	chr20:10225606 - 10225606(1)	intron_variant; non_coding_transcript_variant
rs1013044	chr20:10240396 - 10240396(1)	intron_variant; non_coding_transcript_variant
rs6032829	chr20:10249643 - 10249643(1)	intron_variant; non_coding_transcript_variant
rs363011	chr20:10236688 - 10236688(1)	intron_variant; non_coding_transcript_variant
rs363031	chr20:10237507 - 10237507(1)	intron_variant; non_coding_transcript_variant
rs1158827	chr20:10232894 - 10232894(1)	intron_variant; non_coding_transcript_variant
rs6077697	chr20:10235400 - 10235400(1)	intron_variant; non_coding_transcript_variant
rs362592	chr20:10291844 - 10291844(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs362590	chr20:10290469 - 10290469(1)	intron_variant; non_coding_transcript_variant
rs2284300	chr20:10286176 - 10286176(1)	intron_variant; non_coding_transcript_variant
rs2284299	chr20:10285599 - 10285599(1)	intron_variant; non_coding_transcript_variant
rs2284297	chr20:10285249 - 10285249(1)	intron_variant; non_coding_transcript_variant
rs2076240	chr20:10284274 - 10284274(1)	intron_variant; non_coding_transcript_variant
rs6133845	chr20:10283267 - 10283267(1)	intron_variant; non_coding_transcript_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 1)

Variant Name	Variant Type	Location in Gene	No. of Studies (Positive/Negative/Trend)
SNAP25_promoter_SNP1	point mutation	promoter	1 (0/1/0)

Gene related regions (count: 4)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
20p12	chr20:5100000-17900000	4 (0/0/4)
Chr 20	chr20:0-64444167	4 (0/3/1)
20p12.2-12.1	chr20:9200000-17900000	1 (0/1/0)
20p12.2	chr20:9200000-12000000	1 (0/0/1)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Overlap with SZ from cross-disorder studies (count: 0)

Overlap with SZ from candidate gene intersection analysis (count: 7)

Reference	ID in SZGene	Result Category
12610648	36	Negative
20333500	36	Positive
18191416	36	Negative
19806613	36	Positive
18512733	36	Positive
11287790	36	Negative
19132710	36	Positive

Gene relationship with MDD

Overlap with MDD from cross-disorder studies (count: 0)

Overlap with MDD from candidate gene intersection analysis (count: 1)

Reference	Description	Category in MDD	Link in MK4MDD
22339950	Our findings demonstrate significant dysregulation of synaptic function/structure related genes SNAP25, DLG2 (SAP93), and MAP1A, and 2-amino-3-(5-methyl-3-oxo-1,2-oxazol-4-yl)propanoic acid receptor subunit genes GLUR1 and GLUR3	Pos	SNAP25

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Region: chr20:10218830..10307418 View in gBrowse