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SNCA - ENSG00000145335

synuclein alpha

Also known as: NACP, PD1, alpha-synuclein

Location: chr4:90,645,250-90,759,466 reverse strand

Gene Type: protein coding

More information
NCBI Gene
6622
HUGO
HGNC:11138
Ensembl
ENSG00000145335
VEGA
OTTHUMG00000130948
OMIM
163890
UniProtKB
P37840

Genomic Context

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Gene-based Trait Associations

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ADSP WES: Alzheimer's Disease ADSP

Results from gene-level rare and functional variant aggregation tests for association to AD supported by significane of p < 0.5 / #genes.

Individual score test statistics for rare, predicted functional, and loss of function variants colocated with the gene were aggregated to compute gene level p-values.

See NIAGADS Accession NG00065 for more information.

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Accession Population N SNPs p-value Sign. Level rho CMAF CMAC Covariates Variant Filter Caveats
NG00065 European 8 0.013 N/A 1 6.2e-04 13.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP MOD-HIGH N/A
NG00065 European 8 0.017 N/A 1 6.2e-04 13.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 9 0.035 N/A 1 6.5e-04 14.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH N/A
NG00065 Meta 9 0.045 N/A 1 6.5e-04 14.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP MOD-HIGH N/A
NG00065 European 8 0.094 N/A 1 6.2e-04 13.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 9 0.162 N/A 1 6.5e-04 14.0 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Caribbean Hispanic 1 0.450 N/A 0 1.3e-03 1.0 PCs, sequencing center, sex, age at AD onset or last-known dementia-free age (for controls), and APOE E2 and E4 genotypes VEP MOD-HIGH
NG00065 Caribbean Hispanic 1 0.458 N/A 0 1.3e-03 1.0 PCs and sequencing center VEP MOD-HIGH
NG00065 Caribbean Hispanic 1 0.466 N/A 0 1.3e-03 1.0 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the SNCA gene.

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The SNCA gene contains 5,862 variants records (corresponding to 5,609 unique genomic positions).

The following variants, contained within ±100kb of SNCA, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of SNCA that have genome-wide significance in a NIAGADS Alzheimer's Disease GWAS summary statistics dataset; supported by a p-value < 5 x 10-8. For exome array studies, a cutoff of p-value < 1 x 10-3 was used.

Click on accession numbers to view a detailed report about the dataset or to request access to the data.

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of SNCA that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of SNCA, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of SNCA that have genome-wide significance in a NIAGADS GWAS summary statistics dataset; supported by a p-value < 5 x 10-8. For exome array studies, a cutoff of p-value < 1 x 10-3 was used.

Click on accession numbers to view a detailed report about the dataset or to request access to the data.

NHGRI GWAS: Other Traits (incl. related neuropathologies and AD biomarkers)

Variants contained within ±100kb of SNCA that are associated with a trait in the NHGRI GWAS Catalog.

Functional Genomics

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Explore all functional genomics annotations within the region of the SNCA gene (chr4:90645250-90759466)

Transcription Factor Binding Site Overlap in Gene Promoter Region (ENCODE ChIP-SEQ)

ChIP-Seq sites for transcription factor binding (from selected brain-relevant ENCODE tracks) within the promoter region of this gene. See methods for more information.

Functional Annotation

Gene Ontology

Functional annotations were obtained from UniProt-GOA gene association files.

Click on a term accession number to view term details at the Gene Ontology Consortium.

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Ontology GO Accession Term Evidence Code
BP GO:0006919 activation of cysteine-type endopeptidase activity involved in apoptotic process IDA
BP GO:0008344 adult locomotory behavior IEA
BP GO:0007568 aging IEA
BP GO:0006915 apoptotic process IEA
BP GO:0048148 behavioral response to cocaine IEA
BP GO:0055074 calcium ion homeostasis IDA
BP GO:0044267 cellular protein metabolic process TAS
BP GO:0071280 cellular response to copper ion IDA
BP GO:0071872 cellular response to epinephrine stimulus TAS
BP GO:0044344 cellular response to fibroblast growth factor stimulus IEA
BP GO:0034599 cellular response to oxidative stress IEA,IC
BP GO:0007268 chemical synaptic transmission IEA
BP GO:0042416 dopamine biosynthetic process TAS,IEA
BP GO:0042417 dopamine metabolic process IEA
BP GO:0051583 dopamine uptake involved in synaptic transmission TAS
BP GO:0060079 excitatory postsynaptic potential IEA
BP GO:0006631 fatty acid metabolic process IEA
BP GO:0097435 fibril organization TAS
BP GO:0060291 long-term synaptic potentiation IEA
BP GO:0061024 membrane organization IEA
BP GO:0001774 microglial cell activation TAS,IEA
BP GO:0042775 mitochondrial ATP synthesis coupled electron transport IEA
BP GO:0007006 mitochondrial membrane organization IEA
BP GO:0043066 negative regulation of apoptotic process IMP
BP GO:1904715 negative regulation of chaperone-mediated autophagy IMP
BP GO:0043154 negative regulation of cysteine-type endopeptidase activity involved in apoptotic process IMP
BP GO:0045963 negative regulation of dopamine metabolic process IEA
BP GO:0051585 negative regulation of dopamine uptake involved in synaptic transmission IDA
BP GO:0045920 negative regulation of exocytosis IMP
BP GO:0035067 negative regulation of histone acetylation IDA
BP GO:0031115 negative regulation of microtubule polymerization IDA
BP GO:1902957 negative regulation of mitochondrial electron transport, NADH to ubiquinone TAS
BP GO:0032769 negative regulation of monooxygenase activity IDA
BP GO:0043524 negative regulation of neuron apoptotic process IEA
BP GO:1901215 negative regulation of neuron death IDA
BP GO:0051622 negative regulation of norepinephrine uptake IDA
BP GO:0010642 negative regulation of platelet-derived growth factor receptor signaling pathway IDA
BP GO:0001933 negative regulation of protein phosphorylation IEA
BP GO:0051612 negative regulation of serotonin uptake IDA
BP GO:0070495 negative regulation of thrombin-activated receptor signaling pathway IDA
BP GO:0000122 negative regulation of transcription from RNA polymerase II promoter TAS
BP GO:0032410 negative regulation of transporter activity IDA
BP GO:0006638 neutral lipid metabolic process IEA
BP GO:0055114 oxidation-reduction process IDA
BP GO:0006644 phospholipid metabolic process IEA
BP GO:0043065 positive regulation of apoptotic process TAS
BP GO:0045807 positive regulation of endocytosis IDA
BP GO:1903284 positive regulation of glutathione peroxidase activity IDA
BP GO:1903285 positive regulation of hydrogen peroxide catabolic process IDA
BP GO:0060732 positive regulation of inositol phosphate biosynthetic process IDA
BP GO:0001956 positive regulation of neurotransmitter secretion IEA
BP GO:0033138 positive regulation of peptidyl-serine phosphorylation IEA,ISS
BP GO:0071902 positive regulation of protein serine/threonine kinase activity IDA
BP GO:0001921 positive regulation of receptor recycling IDA
BP GO:0051281 positive regulation of release of sequestered calcium ion into cytosol IDA
BP GO:0050806 positive regulation of synaptic transmission IEA
BP GO:0031648 protein destabilization IDA
BP GO:0031623 receptor internalization IDA
BP GO:0050812 regulation of acyl-CoA biosynthetic process IEA
BP GO:0014059 regulation of dopamine secretion IEA,TAS
BP GO:0014048 regulation of glutamate secretion IEA
BP GO:0040012 regulation of locomotion IEA
BP GO:0048169 regulation of long-term neuronal synaptic plasticity IEA
BP GO:0043030 regulation of macrophage activation IEA
BP GO:0048168 regulation of neuronal synaptic plasticity IEA
BP GO:1901214 regulation of neuron death IEA
BP GO:0046928 regulation of neurotransmitter secretion IEA
BP GO:0010517 regulation of phospholipase activity IDA
BP GO:1903426 regulation of reactive oxygen species biosynthetic process TAS
BP GO:2000377 regulation of reactive oxygen species metabolic process IEA
BP GO:1903421 regulation of synaptic vesicle recycling TAS
BP GO:0042220 response to cocaine IEA
BP GO:0042493 response to drug IEA
BP GO:0034341 response to interferon-gamma IDA
BP GO:0070555 response to interleukin-1 IDA
BP GO:0010040 response to iron(II) ion IDA
BP GO:0032496 response to lipopolysaccharide IDA
BP GO:0032026 response to magnesium ion IDA
BP GO:0050808 synapse organization IEA
BP GO:0001963 synaptic transmission, dopaminergic IEA
BP GO:0048488 synaptic vesicle endocytosis ISS,IEA
BP GO:0048489 synaptic vesicle transport IEA
CC GO:0015629 actin cytoskeleton IDA
CC GO:0030424 axon IDA
CC GO:0043679 axon terminus IEA
CC GO:0005938 cell cortex IDA
CC GO:0030054 cell junction IEA
CC GO:0005737 cytoplasm IDA,IEA
CC GO:0030659 cytoplasmic vesicle membrane IEA
CC GO:0005856 cytoskeleton IEA
CC GO:0005829 cytosol IDA,IEA,TAS
CC GO:0005576 extracellular region IEA,TAS,IDA
CC GO:0005615 extracellular space IDA
CC GO:0005794 Golgi apparatus IEA
CC GO:0030426 growth cone IEA,IDA
CC GO:0016234 inclusion body IDA,IEA
CC GO:0043231 intracellular membrane-bounded organelle IEA
CC GO:0005764 lysosome TAS
CC GO:0016020 membrane IDA,IEA
CC GO:0005747 mitochondrial respiratory chain complex I TAS
CC GO:0005739 mitochondrion TAS,IEA
CC GO:0005640 nuclear outer membrane IEA
CC GO:0005634 nucleus IEA,IDA
CC GO:0048471 perinuclear region of cytoplasm IDA
CC GO:0005886 plasma membrane IEA,IDA
CC GO:0031092 platelet alpha granule membrane IDA
CC GO:0098794 postsynapse IEA
CC GO:0005840 ribosome IEA
CC GO:0005791 rough endoplasmic reticulum IEA
CC GO:0099512 supramolecular fiber IDA
CC GO:0045202 synapse IEA
CC GO:0008021 synaptic vesicle IEA
CC GO:0043195 terminal bouton IEA
MF GO:0043014 alpha-tubulin binding IPI
MF GO:0048487 beta-tubulin binding IEA
MF GO:0005509 calcium ion binding IDA
MF GO:0005507 copper ion binding IDA
MF GO:0043027 cysteine-type endopeptidase inhibitor activity involved in apoptotic process IDA
MF GO:0045502 dynein binding IPI
MF GO:0019899 enzyme binding IEA
MF GO:0005504 fatty acid binding IDA
MF GO:0008198 ferrous iron binding IDA
MF GO:0042393 histone binding IDA,IEA
MF GO:0042802 identical protein binding IPI,IEA,IDA
MF GO:0019894 kinesin binding IPI
MF GO:0000287 magnesium ion binding IDA
MF GO:0046872 metal ion binding IEA
MF GO:0008017 microtubule binding IEA
MF GO:0016491 oxidoreductase activity IDA
MF GO:0043274 phospholipase binding IEA
MF GO:0060961 phospholipase D inhibitor activity IDA
MF GO:0005543 phospholipid binding IDA,IEA
MF GO:0051219 phosphoprotein binding IDA
MF GO:0005515 protein binding IPI
MF GO:0019904 protein domain specific binding IEA
MF GO:0047485 protein N-terminus binding IEA
MF GO:0048156 tau protein binding IDA
MF GO:0044212 transcription regulatory region DNA binding TAS
MF GO:0008270 zinc ion binding IDA

KEGG Pathways

Click on a pathway accession number to view term details at KEGG.

Click on the number in the Find Similar column to get a list of genes annotated by the associated pathway.

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Pathway KEGG Accession Graph
Alzheimer's disease hsa05010
Parkinson's disease hsa05012