PSMB4 (proteasome 20S subunit beta 4)

Download as csv Download as pdf

Log in to bookmark this gene

Bookmark This Gene

Title Project / Tag (optional) Note (optional)

Cancel Save

On this page

Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 5692
• Gene name: Proteasome 20S subunit beta 4
• Gene symbol: PSMB4
• Synonyms (NCBI Gene): HN3, HsN3, PRAAS3, PROS-26, PROS26
• Chromosome: 1
• Chromosome location: 1q21.3
• Summary: The proteasome is a multicatalytic proteinase complex with a highly ordered ring-shaped 20S core structure. The core structure is composed of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha subunits and 2 rings are composed of 7 beta

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs200946642	G>A,T	Pathogenic	5 prime UTR variant
rs1235715459	->G	Pathogenic	Coding sequence variant, frameshift variant
rs1553209362	CTTAGTAGA>-	Pathogenic	Coding sequence variant, inframe deletion
rs1553209373	C>A	Pathogenic	Coding sequence variant, stop gained

miRNA Show/Hide all (40)

miRTarBase ID	miRNA	Experiments	Reference
MIRT050351	hsa-miR-25-3p	CLASH	23622248
MIRT1270234	hsa-miR-1261	CLIP-seq
MIRT1270235	hsa-miR-1299	CLIP-seq
MIRT1270236	hsa-miR-3545-3p	CLIP-seq
MIRT1270237	hsa-miR-3973	CLIP-seq
MIRT1270238	hsa-miR-4277	CLIP-seq
MIRT1270239	hsa-miR-4436b-3p	CLIP-seq
MIRT1270240	hsa-miR-4480	CLIP-seq
MIRT1270241	hsa-miR-4662a-5p	CLIP-seq
MIRT1270242	hsa-miR-4699-3p	CLIP-seq
MIRT1270243	hsa-miR-4742-3p	CLIP-seq
MIRT1270244	hsa-miR-4761-3p	CLIP-seq
MIRT1270245	hsa-miR-4782-5p	CLIP-seq
MIRT1270246	hsa-miR-516b	CLIP-seq
MIRT1270247	hsa-miR-520d-5p	CLIP-seq
MIRT1270248	hsa-miR-520g	CLIP-seq
MIRT1270249	hsa-miR-520h	CLIP-seq
MIRT1270250	hsa-miR-524-5p	CLIP-seq
MIRT1270251	hsa-miR-548n	CLIP-seq
MIRT1270252	hsa-miR-548t	CLIP-seq
MIRT1270253	hsa-miR-891b	CLIP-seq
MIRT1270234	hsa-miR-1261	CLIP-seq
MIRT1270235	hsa-miR-1299	CLIP-seq
MIRT1270238	hsa-miR-4277	CLIP-seq
MIRT1270239	hsa-miR-4436b-3p	CLIP-seq
MIRT1270243	hsa-miR-4742-3p	CLIP-seq
MIRT1270244	hsa-miR-4761-3p	CLIP-seq
MIRT1270245	hsa-miR-4782-5p	CLIP-seq
MIRT1270246	hsa-miR-516b	CLIP-seq
MIRT1270253	hsa-miR-891b	CLIP-seq
MIRT1270234	hsa-miR-1261	CLIP-seq
MIRT1270235	hsa-miR-1299	CLIP-seq
MIRT1270238	hsa-miR-4277	CLIP-seq
MIRT1270239	hsa-miR-4436b-3p	CLIP-seq
MIRT1270243	hsa-miR-4742-3p	CLIP-seq
MIRT1270244	hsa-miR-4761-3p	CLIP-seq
MIRT1270245	hsa-miR-4782-5p	CLIP-seq
MIRT1270246	hsa-miR-516b	CLIP-seq
MIRT1270251	hsa-miR-548n	CLIP-seq
MIRT1270253	hsa-miR-891b	CLIP-seq

Gene ontology (GO) Show/Hide all (30)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000502	Component	Proteasome complex	IDA	17323924, 26524591
GO:0000502	Component	Proteasome complex	IEA
GO:0000502	Component	Proteasome complex	NAS	29636472
GO:0000502	Component	Proteasome complex	TAS	8811196
GO:0001530	Function	Lipopolysaccharide binding	IEA
GO:0002862	Process	Negative regulation of inflammatory response to antigenic stimulus	IEA
GO:0005515	Function	Protein binding	IPI	15231748, 17189198, 17948026, 25416956, 28514442, 31473102, 32296183, 32814053, 33961781, 35271311
GO:0005634	Component	Nucleus	HDA	21630459
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	34711951
GO:0005634	Component	Nucleus	IEA
GO:0005634	Component	Nucleus	TAS	16130169
GO:0005654	Component	Nucleoplasm	IDA
GO:0005654	Component	Nucleoplasm	TAS
GO:0005737	Component	Cytoplasm	IDA	34711951
GO:0005737	Component	Cytoplasm	IEA
GO:0005739	Component	Mitochondrion	IDA
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	TAS
GO:0005839	Component	Proteasome core complex	IDA	34711951
GO:0005839	Component	Proteasome core complex	IEA
GO:0005839	Component	Proteasome core complex	ISS
GO:0019774	Component	Proteasome core complex, beta-subunit complex	IBA
GO:0019774	Component	Proteasome core complex, beta-subunit complex	ISS
GO:0036064	Component	Ciliary basal body	IDA	29257953
GO:0043161	Process	Proteasome-mediated ubiquitin-dependent protein catabolic process	IBA
GO:0043161	Process	Proteasome-mediated ubiquitin-dependent protein catabolic process	IMP	26524591
GO:0043161	Process	Proteasome-mediated ubiquitin-dependent protein catabolic process	NAS	19489727
GO:0051603	Process	Proteolysis involved in protein catabolic process	IEA
GO:0070062	Component	Extracellular exosome	HDA	20458337

Other IDs

• MIM: 602177
• HGNC: 9541
• e!Ensembl: ENSG00000159377

Protein

• UniProt ID: P28070
• Protein name: Proteasome subunit beta type-4 (26 kDa prosomal protein) (HsBPROS26) (PROS-26) (Macropain beta chain) (Multicatalytic endopeptidase complex beta chain) (Proteasome beta chain) (Proteasome chain 3) (HsN3) (Proteasome subunit beta-7) (beta-7)
• Protein function: Non-catalytic component of the 20S core proteasome complex involved in the proteolytic degradation of most intracellular proteins. This complex plays numerous essential roles within the cell by associating with different regulatory particles. As
• PDB: 4R3O , 4R67 , 5A0Q , 5GJQ , 5GJR , 5L4G , 5LE5 , 5LEX , 5LEY , 5LEZ , 5LF0 , 5LF1 , 5LF3 , 5LF4 , 5LF6 , 5LF7 , 5LN3 , 5M32 , 5T0C , 5T0G , 5T0H , 5T0I , 5T0J , 5VFO , 5VFP , 5VFQ , 5VFR , 5VFS , 5VFT , 5VFU , 6AVO , 6E5B , 6KWY , 6MSB , 6MSD , 6MSE , 6MSG , 6MSH , 6MSJ , 6MSK , 6R70 , 6REY , 6RGQ , 6WJD , 6WJN , 6XMJ , 7AWE , 7B12 , 7LXV , 7NAN , 7NAO
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00227	Proteasome	50 → 237	Proteasome subunit	Domain

• Sequence:

  MEAFLGSRSGLWAGGPAPGQFYRIPSTPDSFMDPASALYRGPITRTQNPMVTGTSVLGVK
  FEGGVVIAADMLGSYGSLARFRNISRIMRVNNSTMLGASGDYADFQYLKQVLGQMVIDEE
  LLGDGHSYSPRAIHSWLTRAMYSRRSKMNPLWNTMVIGGYADGESFLGYVDMLGVAYEAP
  SLATGYGAYLAQPLLREVLEKQPVLSQTEARDLVERCMRVLYYRDARSYNRFQIATVTEK
  GVEIEGPLSTETNWDIAHMISGFE

• Sequence length: 264

Pathways

KEGG Pathway	Reactome Pathway
Proteasome	Activation of NF-kappaB in B cells
Alzheimer disease	Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha
Parkinson disease	Cross-presentation of soluble exogenous antigens (endosomes)
Amyotrophic lateral sclerosis	Autodegradation of Cdh1 by Cdh1:APC/C
Huntington disease	SCF-beta-TrCP mediated degradation of Emi1
Spinocerebellar ataxia	APC/C:Cdc20 mediated degradation of Securin
Prion disease	APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1
Pathways of neurodegeneration - multiple diseases	Cdc20:Phospho-APC/C mediated degradation of Cyclin A
	Vpu mediated degradation of CD4
	Vif-mediated degradation of APOBEC3G
	SCF(Skp2)-mediated degradation of p27/p21
	Degradation of beta-catenin by the destruction complex
	Downstream TCR signaling
	Separation of Sister Chromatids
	FCERI mediated NF-kB activation
	Autodegradation of the E3 ubiquitin ligase COP1
	Regulation of ornithine decarboxylase (ODC)
	ABC-family proteins mediated transport
	AUF1 (hnRNP D0) binds and destabilizes mRNA
	Asymmetric localization of PCP proteins
	Degradation of AXIN
	Degradation of DVL
	Hedgehog ligand biogenesis
	Hh mutants that don't undergo autocatalytic processing are degraded by ERAD
	Dectin-1 mediated noncanonical NF-kB signaling
	CLEC7A (Dectin-1) signaling
	Degradation of GLI1 by the proteasome
	GLI3 is processed to GLI3R by the proteasome
	Hedgehog 'on' state
	Regulation of RAS by GAPs
	TNFR2 non-canonical NF-kB pathway
	NIK-->noncanonical NF-kB signaling
	Defective CFTR causes cystic fibrosis
	MAPK6/MAPK4 signaling
	UCH proteinases
	Ub-specific processing proteases
	CDT1 association with the CDC6:ORC:origin complex
	Orc1 removal from chromatin
	CDK-mediated phosphorylation and removal of Cdc6
	G2/M Checkpoints
	Ubiquitin Mediated Degradation of Phosphorylated Cdc25A
	Ubiquitin-dependent degradation of Cyclin D
	The role of GTSE1 in G2/M progression after G2 checkpoint
	FBXL7 down-regulates AURKA during mitotic entry and in early mitosis
	RUNX1 regulates transcription of genes involved in differentiation of HSCs
	Regulation of RUNX2 expression and activity
	Regulation of RUNX3 expression and activity
	Regulation of PTEN stability and activity
	Neddylation
	Interleukin-1 signaling
	Antigen processing: Ubiquitination & Proteasome degradation

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
Proteasome-associated autoinflammatory syndrome 1	Pathogenic	rs1553209373	RCV000663378	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Proteasome-associated autoinflammatory syndrome 3	Pathogenic	rs1553209362	RCV000663375	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations Show/Hide Unknown Diseases (7)
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
CANDLE SYNDROME	—	Disgenet	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MAJOR DEPRESSIVE DISORDER	—	Disgenet, GWAS catalog Disgenet, GWAS catalog	29662059	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MYOCARDIAL INFARCTION	—	GWAS catalog	38072966	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PSMB4-related disorder	Benign; Uncertain significance; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TYPE 2 DIABETES MELLITUS	—	GWAS catalog	38374256	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
UNIPOLAR DEPRESSION	—	Disgenet	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining Show/Hide Text Mining Associations (34)
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Acanthosis Nigricans	Acanthosis Nigricans	HPO_DG			★☆☆☆☆ Found in Text Mining only
Anemia	Anemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Arthritis	Arthritis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Arthritis Rheumatoid	Rheumatoid arthritis	Pubtator	39342401	Associate	★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	BEFREE	30066880		★☆☆☆☆ Found in Text Mining only
Carcinoma Hepatocellular	Hepatocellular carcinoma	Pubtator	36062301	Associate	★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	35693739	Stimulate	★☆☆☆☆ Found in Text Mining only
Carcinoma, Ovarian Epithelial	Ovarian Epithelial carcinoma	BEFREE	26439929		★☆☆☆☆ Found in Text Mining only
cervical cancer	Cervical Cancer	BEFREE	31699366		★☆☆☆☆ Found in Text Mining only
Cervix carcinoma	Cervix carcinoma	BEFREE	31699366		★☆☆☆☆ Found in Text Mining only

Related Genes

Sort by: Blended Diseases Pathways Evidence source

PSMB8 2 shared diseasesCandle syndrome, Proteasome associated autoinflammatory syndrome 51 shared pathwaysProteasome, Regulation of PTEN stability and activity, Ub-specific processing proteases, Neddylation, Separation of Sister Chromatids, ABC-family proteins mediated transport, Regulation of RAS by GAPs, SCF(Skp2)-mediated degradation of p27/p21, Orc1 removal from chromatin, CDK-mediated phosphorylation and removal of Cdc6, Ubiquitin-dependent degradation of Cyclin D, Activation of NF-kappaB in B cells +39 more 4 shared evidence sourcesDisgenet (Candle syndrome), ClinVar (Proteasome associated autoinflammatory syndrome), HPO (Proteasome associated autoinflammatory syndrome), Disgenet (Proteasome associated autoinflammatory syndrome) Related via 51 shared pathways including Proteasome, Regulation of PTEN stability and activity — evidence mostly Disgenet. PSMB9 1 shared diseaseProteasome associated autoinflammatory syndrome 51 shared pathwaysProteasome, Regulation of PTEN stability and activity, Ub-specific processing proteases, Neddylation, Separation of Sister Chromatids, ABC-family proteins mediated transport, Regulation of RAS by GAPs, SCF(Skp2)-mediated degradation of p27/p21, Orc1 removal from chromatin, CDK-mediated phosphorylation and removal of Cdc6, Ubiquitin-dependent degradation of Cyclin D, Activation of NF-kappaB in B cells +39 more 4 shared evidence sourcesClinVar (Proteasome associated autoinflammatory syndrome), HPO (Proteasome associated autoinflammatory syndrome), Disgenet (Proteasome associated autoinflammatory syndrome), GenCC (Proteasome associated autoinflammatory syndrome) Related via 51 shared pathways including Proteasome, Regulation of PTEN stability and activity — evidence mostly ClinVar. PSMB10 1 shared diseaseProteasome associated autoinflammatory syndrome 51 shared pathwaysProteasome, Regulation of PTEN stability and activity, Ub-specific processing proteases, Neddylation, Separation of Sister Chromatids, ABC-family proteins mediated transport, Regulation of RAS by GAPs, SCF(Skp2)-mediated degradation of p27/p21, Orc1 removal from chromatin, CDK-mediated phosphorylation and removal of Cdc6, Ubiquitin-dependent degradation of Cyclin D, Activation of NF-kappaB in B cells +39 more 3 shared evidence sourcesClinVar (Proteasome associated autoinflammatory syndrome), HPO (Proteasome associated autoinflammatory syndrome), Disgenet (Proteasome associated autoinflammatory syndrome) Related via 51 shared pathways including Proteasome, Regulation of PTEN stability and activity — evidence mostly ClinVar. PSMA3 1 shared diseaseProteasome associated autoinflammatory syndrome 54 shared pathwaysProteasome, Parkinson disease, Spinocerebellar ataxia, Prion disease, Regulation of PTEN stability and activity, Ub-specific processing proteases, Neddylation, Separation of Sister Chromatids, ABC-family proteins mediated transport, Regulation of RAS by GAPs, SCF(Skp2)-mediated degradation of p27/p21, Orc1 removal from chromatin +42 more 1 shared evidence sourceDisgenet (Proteasome associated autoinflammatory syndrome) Related via 54 shared pathways including Proteasome, Parkinson disease — evidence mostly Disgenet. PSMA1 54 shared pathwaysProteasome, Parkinson disease, Spinocerebellar ataxia, Prion disease, Regulation of PTEN stability and activity, Ub-specific processing proteases, Neddylation, Separation of Sister Chromatids, ABC-family proteins mediated transport, Regulation of RAS by GAPs, SCF(Skp2)-mediated degradation of p27/p21, Orc1 removal from chromatin +42 more Related via 54 shared pathways including Proteasome, Parkinson disease.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
PSMB8	2	["Candle syndrome","Proteasome associated autoinflammatory syndrome"]	51	["Proteasome","Regulation of PTEN stability and activity","Ub-specific processing proteases","Neddylation","Separation of Sister Chromatids","ABC-family proteins mediated transport","Regulation of RAS by GAPs","SCF(Skp2)-mediated degradation of p27\/p21","Orc1 removal from chromatin","CDK-mediated phosphorylation and removal of Cdc6","Ubiquitin-dependent degradation of Cyclin D","Activation of NF-kappaB in B cells"]	4	["Disgenet (Candle syndrome)","ClinVar (Proteasome associated autoinflammatory syndrome)","HPO (Proteasome associated autoinflammatory syndrome)","Disgenet (Proteasome associated autoinflammatory syndrome)"]
PSMB9	1	["Proteasome associated autoinflammatory syndrome"]	51	["Proteasome","Regulation of PTEN stability and activity","Ub-specific processing proteases","Neddylation","Separation of Sister Chromatids","ABC-family proteins mediated transport","Regulation of RAS by GAPs","SCF(Skp2)-mediated degradation of p27\/p21","Orc1 removal from chromatin","CDK-mediated phosphorylation and removal of Cdc6","Ubiquitin-dependent degradation of Cyclin D","Activation of NF-kappaB in B cells"]	4	["ClinVar (Proteasome associated autoinflammatory syndrome)","HPO (Proteasome associated autoinflammatory syndrome)","Disgenet (Proteasome associated autoinflammatory syndrome)","GenCC (Proteasome associated autoinflammatory syndrome)"]
PSMB10	1	["Proteasome associated autoinflammatory syndrome"]	51	["Proteasome","Regulation of PTEN stability and activity","Ub-specific processing proteases","Neddylation","Separation of Sister Chromatids","ABC-family proteins mediated transport","Regulation of RAS by GAPs","SCF(Skp2)-mediated degradation of p27\/p21","Orc1 removal from chromatin","CDK-mediated phosphorylation and removal of Cdc6","Ubiquitin-dependent degradation of Cyclin D","Activation of NF-kappaB in B cells"]	3	["ClinVar (Proteasome associated autoinflammatory syndrome)","HPO (Proteasome associated autoinflammatory syndrome)","Disgenet (Proteasome associated autoinflammatory syndrome)"]
PSMA3	1	["Proteasome associated autoinflammatory syndrome"]	54	["Proteasome","Parkinson disease","Spinocerebellar ataxia","Prion disease","Regulation of PTEN stability and activity","Ub-specific processing proteases","Neddylation","Separation of Sister Chromatids","ABC-family proteins mediated transport","Regulation of RAS by GAPs","SCF(Skp2)-mediated degradation of p27\/p21","Orc1 removal from chromatin"]	1	["Disgenet (Proteasome associated autoinflammatory syndrome)"]
PSMA1	0	[]	54	["Proteasome","Parkinson disease","Spinocerebellar ataxia","Prion disease","Regulation of PTEN stability and activity","Ub-specific processing proteases","Neddylation","Separation of Sister Chromatids","ABC-family proteins mediated transport","Regulation of RAS by GAPs","SCF(Skp2)-mediated degradation of p27\/p21","Orc1 removal from chromatin"]	0	[]

Diseases Linked via Similar Genes

Hypothyroidism Linked via 2 of 5 related genesPSMB8, PSMB9 Rheumatoid arthritis Linked via 2 of 5 related genesPSMB8, PSMB9 Systemic lupus erythematosus Linked via 2 of 5 related genesPSMB8, PSMB9 Diabetes mellitus type 1 Linked via 2 of 5 related genesPSMB8, PSMB9 Autoinflammatory syndrome Linked via 1 of 5 related genesPSMB8

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Hypothyroidism	2	["PSMB8","PSMB9"]
Rheumatoid arthritis	2	["PSMB8","PSMB9"]
Systemic lupus erythematosus	2	["PSMB8","PSMB9"]
Diabetes mellitus type 1	2	["PSMB8","PSMB9"]
Autoinflammatory syndrome	1	["PSMB8"]