Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Transcription factors Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	6620
Gene name	Synuclein beta
Gene symbol	SNCB
Synonyms (NCBI Gene)	-
Chromosome	5
Chromosome location	5q35.2
Summary	This gene encodes a member of a small family of proteins that inhibit phospholipase D2 and may function in neuronal plasticity. The encoded protein is abundant in lesions of patients with Alzheimer disease. A mutation in this gene was found in individuals

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SNP ID	Visualize variation	Clinical significance	Consequence
rs104893936	C>G,T	Pathogenic	Coding sequence variant, missense variant
rs104893937	G>T	Pathogenic	Intron variant, coding sequence variant, missense variant

Show/Hide all (66)

miRTarBase ID	miRNA	Experiments	Reference
MIRT018267	hsa-miR-335-5p	Microarray	18185580
MIRT544945	hsa-miR-548ac	PAR-CLIP	21572407
MIRT544944	hsa-miR-548bb-3p	PAR-CLIP	21572407
MIRT544943	hsa-miR-548d-3p	PAR-CLIP	21572407
MIRT544942	hsa-miR-548h-3p	PAR-CLIP	21572407
MIRT544941	hsa-miR-548z	PAR-CLIP	21572407
MIRT544940	hsa-miR-548ae-3p	PAR-CLIP	21572407
MIRT544939	hsa-miR-548ah-3p	PAR-CLIP	21572407
MIRT544938	hsa-miR-548aj-3p	PAR-CLIP	21572407
MIRT544937	hsa-miR-548am-3p	PAR-CLIP	21572407
MIRT544936	hsa-miR-548aq-3p	PAR-CLIP	21572407
MIRT544935	hsa-miR-548j-3p	PAR-CLIP	21572407
MIRT544934	hsa-miR-548x-3p	PAR-CLIP	21572407
MIRT544933	hsa-miR-4789-3p	PAR-CLIP	21572407
MIRT544932	hsa-miR-376c-3p	PAR-CLIP	21572407
MIRT544931	hsa-miR-4773	PAR-CLIP	21572407
MIRT544945	hsa-miR-548ac	PAR-CLIP	21572407
MIRT544944	hsa-miR-548bb-3p	PAR-CLIP	21572407
MIRT544943	hsa-miR-548d-3p	PAR-CLIP	21572407
MIRT544942	hsa-miR-548h-3p	PAR-CLIP	21572407
MIRT544941	hsa-miR-548z	PAR-CLIP	21572407
MIRT544940	hsa-miR-548ae-3p	PAR-CLIP	21572407
MIRT544939	hsa-miR-548ah-3p	PAR-CLIP	21572407
MIRT544938	hsa-miR-548aj-3p	PAR-CLIP	21572407
MIRT544937	hsa-miR-548am-3p	PAR-CLIP	21572407
MIRT544936	hsa-miR-548aq-3p	PAR-CLIP	21572407
MIRT544935	hsa-miR-548j-3p	PAR-CLIP	21572407
MIRT544934	hsa-miR-548x-3p	PAR-CLIP	21572407
MIRT544933	hsa-miR-4789-3p	PAR-CLIP	21572407
MIRT544932	hsa-miR-376c-3p	PAR-CLIP	21572407
MIRT544931	hsa-miR-4773	PAR-CLIP	21572407
MIRT1375429	hsa-miR-1324	CLIP-seq
MIRT1375430	hsa-miR-3117-5p	CLIP-seq
MIRT1375431	hsa-miR-3144-5p	CLIP-seq
MIRT1375432	hsa-miR-3191	CLIP-seq
MIRT1375433	hsa-miR-4520a-3p	CLIP-seq
MIRT1375434	hsa-miR-4525	CLIP-seq
MIRT1375435	hsa-miR-4652-5p	CLIP-seq
MIRT1375436	hsa-miR-4717-3p	CLIP-seq
MIRT1375437	hsa-miR-574-3p	CLIP-seq
MIRT1375438	hsa-miR-1207-5p	CLIP-seq
MIRT1375439	hsa-miR-149	CLIP-seq
MIRT1375440	hsa-miR-1908	CLIP-seq
MIRT1375441	hsa-miR-4294	CLIP-seq
MIRT1375442	hsa-miR-4521	CLIP-seq
MIRT1375443	hsa-miR-4763-3p	CLIP-seq
MIRT1375444	hsa-miR-486-3p	CLIP-seq
MIRT1375445	hsa-miR-663	CLIP-seq
MIRT1375446	hsa-miR-744	CLIP-seq
MIRT2111638	hsa-miR-183	CLIP-seq
MIRT2334800	hsa-miR-138	CLIP-seq
MIRT2334801	hsa-miR-218	CLIP-seq
MIRT2334802	hsa-miR-219-2-3p	CLIP-seq
MIRT2334803	hsa-miR-4283	CLIP-seq
MIRT2334804	hsa-miR-4447	CLIP-seq
MIRT2334805	hsa-miR-4456	CLIP-seq
MIRT2334806	hsa-miR-4472	CLIP-seq
MIRT2334807	hsa-miR-4488	CLIP-seq
MIRT2334808	hsa-miR-4697-5p	CLIP-seq
MIRT2334809	hsa-miR-541	CLIP-seq
MIRT2334810	hsa-miR-654-5p	CLIP-seq
MIRT2394914	hsa-miR-136	CLIP-seq
MIRT1375431	hsa-miR-3144-5p	CLIP-seq
MIRT1375432	hsa-miR-3191	CLIP-seq
MIRT1375434	hsa-miR-4525	CLIP-seq
MIRT1375435	hsa-miR-4652-5p	CLIP-seq

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Transcription factor	Regulation	Reference
MTF1	Unknown	21386983

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GO ID	Ontology	Definition	Evidence	Reference
GO:0004859	Function	Phospholipase inhibitor activity	TAS	9806846
GO:0005509	Function	Calcium ion binding	IDA	11312271
GO:0005515	Function	Protein binding	IPI	32296183, 32814053
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	TAS
GO:0007268	Process	Chemical synaptic transmission	IBA
GO:0007268	Process	Chemical synaptic transmission	IEA
GO:0016234	Component	Inclusion body	IDA	17222866
GO:0016234	Component	Inclusion body	IEA
GO:0042417	Process	Dopamine metabolic process	IEA
GO:0043025	Component	Neuronal cell body	IBA
GO:0043524	Process	Negative regulation of neuron apoptotic process	IEA
GO:0043679	Component	Axon terminus	IBA
GO:0045202	Component	Synapse	IEA
GO:0046914	Function	Transition metal ion binding	IMP	25495902
GO:0048488	Process	Synaptic vesicle endocytosis	IBA
GO:0048488	Process	Synaptic vesicle endocytosis	IEA
GO:0050808	Process	Synapse organization	IBA
GO:0050808	Process	Synapse organization	IEA
GO:0051402	Process	Neuron apoptotic process	IEA
GO:1903136	Function	Cuprous ion binding	IBA
GO:1903136	Function	Cuprous ion binding	IEA
GO:1903136	Function	Cuprous ion binding	IMP	25495902

MIM	HGNC	e!Ensembl
602569	11140	ENSG00000074317

Q16143

Protein name

Beta-synuclein

Protein function

Non-amyloid component of senile plaques found in Alzheimer disease. Could act as a regulator of SNCA aggregation process. Protects neurons from staurosporine and 6-hydroxy dopamine (6OHDA)-stimulated caspase activation in a p53/TP53-dependent ma

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01387	Synuclein	1 → 125	Synuclein	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed predominantly in brain; concentrated in presynaptic nerve terminals.

Sequence

MDVFMKGLSMAKEGVVAAAEKTKQGVTEAAEKTKEGVLYVGSKTREGVVQGVASVAEKTK
EQASHLGGAVFSGAGNIAAATGLVKREEFPTDLKPEEVAQEAAEEPLIEPLMEPEGESYE
DPPQEEYQEYEPEA

Sequence length

134

Interactions

View interactions

	Reactome
			MTF1 activates gene expression

Show/Hide Causal Diseases (1)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Lewy body dementia	Pathogenic	rs104893936	RCV000007440

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Malignant tumor of esophagus	Benign	rs4868669	RCV005911380
SNCB-related disorder	Conflicting classifications of pathogenicity; Likely benign	rs104893937, rs377254074	RCV003944805 RCV003954398

Show/Hide Text Mining Associations (17)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Alzheimer Disease	Associate	19072283, 36776048, 40613333
Colorectal Neoplasms	Associate	32453965
Drug Related Side Effects and Adverse Reactions	Associate	29054856, 34254125
Frontotemporal Dementia	Associate	40613333
Glioma	Associate	18474104
Leukemia Erythroblastic Acute	Associate	21264917
Leukemia Megakaryoblastic Acute	Associate	21264917
Lewy Body Disease	Associate	26332674, 40613333
Multiple Sclerosis	Associate	36785484
Multiple System Atrophy	Associate	36785484
Myelodysplastic Syndromes	Associate	21264917
Nerve Degeneration	Associate	9806846
Neurodegenerative Diseases	Associate	9806846
Oligodendroglioma	Associate	14997935
Parkinson Disease	Associate	12239163, 12867415, 17556099, 18436957, 26332674, 9806846
Plaque Amyloid	Stimulate	10619569
Sleep Deprivation	Inhibit	12867415

SNCB (synuclein beta)