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PSMC3 - ENSG00000165916

proteasome 26S subunit, ATPase 3

Also known as: TBP1, TBP-1

Location: chr11:47,440,320-47,447,993 reverse strand

Gene Type: protein coding

More information
NCBI Gene
5702
HUGO
HGNC:9549
Ensembl
ENSG00000165916
VEGA
OTTHUMG00000167692
OMIM
186852
UniProtKB
P17980

Genomic Context

The genome browser snapshot is fully interactive. Mouse over track elements for more information. Click and drag to move tracks. Click and drag on top positional guide to zoom to a sub-region.

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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 7 0.360 N/A 0 3.4e-04 7.1 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH
NG00065 European 7 0.382 N/A 0 3.4e-04 7.1 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 European 7 0.466 N/A 0 3.4e-04 7.1 PCs and sequencing center VEP MOD-HIGH
NG00065 Meta 9 0.653 N/A 0 4.7e-04 10.1 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 0.660 N/A 1 4.7e-04 10.1 PCs and sequencing center VEP MOD-HIGH N/A
NG00065 Meta 9 0.664 N/A 0 4.7e-04 10.1 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 Caribbean Hispanic 2 0.766 N/A 1 3.9e-03 3.1 PCs and sequencing center VEP MOD-HIGH
NG00065 Caribbean Hispanic 2 0.779 N/A 1 3.9e-03 3.1 PCs, sequencing center, sex, and age at AD onset or last-known dementia-free age (for controls) VEP MOD-HIGH
NG00065 Caribbean Hispanic 2 0.809 N/A 1 3.9e-03 3.1 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

Genetic Variation and Variant-based Trait Associations (GWAS)

Variants contained within the PSMC3 gene.

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The PSMC3 gene contains 727 variants records (corresponding to 691 unique genomic positions).

The following variants, contained within ±100kb of PSMC3, have been found to be associated with Alzheimer's disease in a GWAS study:

NIAGADS GWAS: Alzheimer's Disease

Variants contained within ±100kb of PSMC3 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.

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Relative Position Variant ADSP? Allele p-Value Track Accession
upstream N/A 1.3e-8 ADSP Single-Variant Risk Association: Caribbean Hispanic (Model 1) NG00065
upstream N/A 1.3e-8 ADSP Single-Variant Risk Association: European (Model 1) NG00065
upstream G 1.4e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream A 1.9e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream A 2.4e-8 IGAP 2013: Stages 1 and 2 NG00036
in gene A 2.9e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream T 3.0e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream G 3.0e-8 IGAP 2013: Stages 1 and 2 NG00036
downstream C 3.2e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream A 3.5e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream N/A A 3.6e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream A 3.9e-8 IGAP 2013: Stages 1 and 2 NG00036
upstream G 4.3e-8 IGAP 2013: Stages 1 and 2 NG00036

NHGRI GWAS: Alzheimer's Disease

Variants contained within ±100kb of PSMC3 that are associated with Alzheimer's disease in the NHGRI GWAS Catalog.

The following variants, contained within ±100kb of PSMC3, have been associated with AD-relevant neuropathologies in a GWAS study:

NIAGADS GWAS: AD biomarkers and related neuropathologies

Variants contained within ±100kb of PSMC3 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 PSMC3 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 PSMC3 gene (chr11:47440320-47447993)

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:0031145 anaphase-promoting complex-dependent catabolic process TAS
BP GO:0002479 antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent TAS
BP GO:0001824 blastocyst development IEA
BP GO:0030433 ER-associated ubiquitin-dependent protein catabolic process IBA
BP GO:0038095 Fc-epsilon receptor signaling pathway TAS
BP GO:0000165 MAPK cascade TAS
BP GO:0090090 negative regulation of canonical Wnt signaling pathway TAS
BP GO:0010972 negative regulation of G2/M transition of mitotic cell cycle TAS
BP GO:1903507 negative regulation of nucleic acid-templated transcription IEA
BP GO:0051436 negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle TAS
BP GO:0043312 neutrophil degranulation TAS
BP GO:0038061 NIK/NF-kappaB signaling TAS
BP GO:0090263 positive regulation of canonical Wnt signaling pathway TAS
BP GO:1901800 positive regulation of proteasomal protein catabolic process IEA
BP GO:0045899 positive regulation of RNA polymerase II transcriptional preinitiation complex assembly IBA
BP GO:0051437 positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition TAS
BP GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process TAS
BP GO:0030163 protein catabolic process IEA
BP GO:0016579 protein deubiquitination TAS
BP GO:0000209 protein polyubiquitination TAS
BP GO:0006521 regulation of cellular amino acid metabolic process TAS
BP GO:0043488 regulation of mRNA stability TAS
BP GO:0061418 regulation of transcription from RNA polymerase II promoter in response to hypoxia TAS
BP GO:0031146 SCF-dependent proteasomal ubiquitin-dependent protein catabolic process TAS
BP GO:0002223 stimulatory C-type lectin receptor signaling pathway TAS
BP GO:0050852 T cell receptor signaling pathway TAS
BP GO:0055085 transmembrane transport TAS
BP GO:0033209 tumor necrosis factor-mediated signaling pathway TAS
BP GO:0016032 viral process IEA
BP GO:0060071 Wnt signaling pathway, planar cell polarity pathway TAS
CC GO:0005737 cytoplasm IEA
CC GO:0000932 cytoplasmic mRNA processing body ISS,IEA
CC GO:0005829 cytosol TAS
CC GO:0031597 cytosolic proteasome complex IBA
CC GO:0005576 extracellular region TAS
CC GO:1904813 ficolin-1-rich granule lumen TAS
CC GO:0016020 membrane IDA
CC GO:0031595 nuclear proteasome complex IBA
CC GO:0005654 nucleoplasm TAS
CC GO:0005634 nucleus IDA,IEA,TAS
CC GO:0022624 proteasome accessory complex IEA,ISS
CC GO:0000502 proteasome complex IEA,TAS,IDA
CC GO:0008540 proteasome regulatory particle, base subcomplex IBA
CC GO:0034774 secretory granule lumen TAS
MF GO:0016887 ATPase activity ISS
MF GO:0005524 ATP binding IEA
MF GO:0016787 hydrolase activity IEA
MF GO:0042802 identical protein binding IPI
MF GO:0000166 nucleotide binding IEA
MF GO:0036402 proteasome-activating ATPase activity IBA
MF GO:0005515 protein binding IPI
MF GO:0017025 TBP-class protein binding IBA
MF GO:0003713 transcription coactivator activity TAS
MF GO:0003714 transcription corepressor activity TAS

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
Epstein-Barr virus infection hsa05169
Proteasome hsa03050