SNCB (synuclein beta)

Gene

• 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

SNPs

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

miRNA

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

Transcription factors

Transcription factor	Regulation	Reference
MTF1	Unknown	21386983

Gene ontology (GO)

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

Other IDs

• MIM: 602569
• HGNC: 11140
• e!Ensembl: ENSG00000074317

Protein

• UniProt ID: 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

Pathways

Reactome:

MTF1 activates gene expression

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Lewy body dementia	Pathogenic	rs104893936	RCV000007440	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
DEMENTIA, LEWY BODY	—	HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
LEWY BODY DISEASE	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PARKINSON DISEASE	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SCHIZOPHRENIA	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
SNCB-related disorder	Conflicting classifications of pathogenicity; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Adult Oligodendroglioma	Oligodendroglioma	BEFREE	14997935		★☆☆☆☆ Found in Text Mining only
Alpers Syndrome (disorder)	Alpers Syndrome	BEFREE	30787438		★☆☆☆☆ Found in Text Mining only
Alzheimer Disease	Alzheimer disease	Pubtator	19072283, 36776048, 40613333	Associate	★☆☆☆☆ Found in Text Mining only
Autism Spectrum Disorders	Autism Spectrum Disorder	BEFREE	29850516		★☆☆☆☆ Found in Text Mining only
Autistic Disorder	Autism	BEFREE	29850516		★☆☆☆☆ Found in Text Mining only
Autonomic nervous system disorders	Autonomic Central Nervous System Diseases	BEFREE	28871332		★☆☆☆☆ Found in Text Mining only
Autosomal Dominant Parkinsonism	Parkinsonian disease	BEFREE	15136696		★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	11016747, 14504205, 18498014, 9973226		★☆☆☆☆ Found in Text Mining only
cervical cancer	Cervical Cancer	BEFREE	31333726		★☆☆☆☆ Found in Text Mining only
Cervix carcinoma	Cervix carcinoma	BEFREE	31333726		★☆☆☆☆ Found in Text Mining only
Childhood Oligodendroglioma	Oligodendroglioma	BEFREE	14997935		★☆☆☆☆ Found in Text Mining only
Colorectal Carcinoma	Colorectal Cancer	BEFREE	20043104		★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Colorectal neoplasm	Pubtator	32453965	Associate	★☆☆☆☆ Found in Text Mining only
Delusions	Delusions	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dementia	Dementia	BEFREE	20959308, 21683963, 22205345, 28963338, 29278715, 29370097, 29976232		★☆☆☆☆ Found in Text Mining only
Dementia	Dementia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ductal Carcinoma	Ductal Carcinoma	BEFREE	10813729		★☆☆☆☆ Found in Text Mining only
Dysautonomia	Dysautonomia	BEFREE	28871332		★☆☆☆☆ Found in Text Mining only
Encephalitis	Encephalitis	BEFREE	31190448		★☆☆☆☆ Found in Text Mining only
Frontotemporal Dementia	Frontotemporal dementia	Pubtator	40613333	Associate	★☆☆☆☆ Found in Text Mining only
Frontotemporal Lobar Degeneration	Frontotemporal dementia	BEFREE	16651890, 17278999		★☆☆☆☆ Found in Text Mining only
Glioma	Glioma	Pubtator	18474104	Associate	★☆☆☆☆ Found in Text Mining only
Huntington Disease	Huntington Disease	BEFREE	17176119		★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	BEFREE	20232069, 29046879, 30089615		★☆☆☆☆ Found in Text Mining only
Lafora Disease	Lafora Disease	BEFREE	11578596, 29278715		★☆☆☆☆ Found in Text Mining only
Lewy Body Disease	Lewy Body Disease	BEFREE	11890854, 15365127, 15483670, 16847063, 17652097, 20697047, 20959308, 22205345, 25996784, 29278715, 29370097, 30040713, 30154934		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lewy Body Disease	Lewy Body Disease	GENOMICS_ENGLAND_DG	21045828		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lewy Body Disease	Lewy body disease	Pubtator	26332674, 40613333	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lewy Body Disease	Lewy Body Disease	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lewy Body Disease	Lewy Body Disease	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant neoplasm of breast	Breast Cancer	BEFREE	14504205, 18498014, 9973226		★☆☆☆☆ Found in Text Mining only
Malignant Neoplasms	Malignant Neoplasm	BEFREE	25142230, 31333726		★☆☆☆☆ Found in Text Mining only
Malignant tumor of cervix	Cervical Tumor	BEFREE	31333726		★☆☆☆☆ Found in Text Mining only
Medulloblastoma	Medulloblastoma	LHGDN	12783249		★☆☆☆☆ Found in Text Mining only
Movement Disorders	Movement Disorders	BEFREE	29370097		★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple Sclerosis	BEFREE	31190448, 31689443		★☆☆☆☆ Found in Text Mining only
Multiple Sclerosis	Multiple sclerosis	Pubtator	36785484	Associate	★☆☆☆☆ Found in Text Mining only
Multiple System Atrophy	Multiple system atrophy	Pubtator	36785484	Associate	★☆☆☆☆ Found in Text Mining only
Myelodysplastic Syndromes	Myelodysplastic syndrome	Pubtator	21264917	Associate	★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	16432078, 20043104, 31333726		★☆☆☆☆ Found in Text Mining only
Neuroblastoma	Neuroblastoma	BEFREE	19711118		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Neurodegenerative disorder	Pubtator	9806846	Associate	★☆☆☆☆ Found in Text Mining only
Neurodegenerative Disorders	Neurodegenerative Disorders	BEFREE	10192768, 11578596, 11683992, 12428718, 12761628, 12869803, 15123735, 15314265, 15455441, 16489609, 18220522, 18353371, 20522010, 20854101, 28673288, 28913005, 28963338, 29808713, 29976232, 30154934, 31128101, 31281579		★☆☆☆☆ Found in Text Mining only
NON RARE IN EUROPE: Dementia with Lewy body	Dementia With Lewy Body	Orphanet			★☆☆☆☆ Found in Text Mining only
oligodendroglioma	Oligodendroglioma	BEFREE	14997935		★☆☆☆☆ Found in Text Mining only
Oligodendroglioma	Oligodendroglioma	Pubtator	14997935	Associate	★☆☆☆☆ Found in Text Mining only
Parkinson Disease	Parkinson disease	BEFREE	10192768, 10430516, 10469843, 11683992, 11959424, 12025860, 12428718, 12846984, 15033366, 15365127, 15460447, 15483670, 16175160, 16847063, 16959793, 17209570, 17319280, 17448146, 17556099, 18436957, 19081538, 19351880, 20522009, 20522010, 20697047, 20959308, 21085664, 21683963, 22205345, 22275250, 23512373, 24145820, 24204929, 24403142, 24879013, 26332674, 26438087, 26501339, 26924014, 27509067, 27538639, 28133550, 28220836, 28282812, 28430289, 28634349, 28673288, 28710275, 28820253, 28836226, 28887374, 28913005, 28928221, 28963338, 29046879, 29149290, 29214093, 29263407, 29333317, 29364143, 29370097, 29434298, 29782835, 29804260, 29849887, 29850629, 30040713, 30089615, 30107604, 30185079, 30248065, 30536337, 30562735, 30741691, 30941047, 30944722, 31020003, 31048127, 31091335, 31182996, 31191899, 31211166, 31309116, 31389332, 31441047, 31601400, 31687080, 31812666		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Parkinson Disease	Parkinson disease	Pubtator	12239163, 12867415, 17556099, 18436957, 26332674, 9806846	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Parkinson Disease	Parkinson disease	LHGDN	12867415		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Parkinsonian Disorders	Parkinson Disease	BEFREE	10599788, 14736756, 16489609, 9728955		★☆☆☆☆ Found in Text Mining only
Parkinsonian Disorders	Parkinson Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pervasive Development Disorder	Autism spectrum disorder	BEFREE	29850516		★☆☆☆☆ Found in Text Mining only
Presenile dementia	Senile Dementia	BEFREE	20959308, 21683963, 22205345, 28963338, 29278715, 29370097, 29976232		★☆☆☆☆ Found in Text Mining only
Sandhoff Disease	Sandhoff Disease	BEFREE	17653558		★☆☆☆☆ Found in Text Mining only
Sandhoff Disease	Sandhoff Disease	LHGDN	17653558		★☆☆☆☆ Found in Text Mining only
Schizophrenia	Schizophrenia	BEFREE	20854101		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Schizophrenia	Schizophrenia	PSYGENET_DG	20854101		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Senile Plaques	Senile Plaques	BEFREE	8759778		★☆☆☆☆ Found in Text Mining only
Sleep Apnea, Obstructive	Sleep Apnea	BEFREE	31020003		★☆☆☆☆ Found in Text Mining only
Sleep Deprivation	Sleep deprivation	Pubtator	12867415	Inhibit	★☆☆☆☆ Found in Text Mining only
Well Differentiated Oligodendroglioma	Oligodendroglioma	BEFREE	14997935		★☆☆☆☆ Found in Text Mining only
Young onset Parkinson disease	Parkinson disease	BEFREE	10348463		★☆☆☆☆ Found in Text Mining only