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PSMD12 proteasome 26S subunit, non-ATPase 12 [ Homo sapiens (human) ]

Gene ID: 5718, updated on 27-Nov-2024

Summary

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Official Symbol
PSMD12provided by HGNC
Official Full Name
proteasome 26S subunit, non-ATPase 12provided by HGNC
Primary source
HGNC:HGNC:9557
See related
Ensembl:ENSG00000197170 MIM:604450; AllianceGenome:HGNC:9557
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
p55; Rpn5; STISS
Summary
The 26S proteasome is a multicatalytic proteinase complex with a highly ordered structure composed of 2 complexes, a 20S core and a 19S regulator. The 20S core 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 subunits. The 19S regulator is composed of a base, which contains 6 ATPase subunits and 2 non-ATPase subunits, and a lid, which contains up to 10 non-ATPase subunits. Proteasomes are distributed throughout eukaryotic cells at a high concentration and cleave peptides in an ATP/ubiquitin-dependent process in a non-lysosomal pathway. An essential function of a modified proteasome, the immunoproteasome, is the processing of class I MHC peptides. This gene encodes a non-ATPase subunit of the 19S regulator. A pseudogene has been identified on chromosome 3. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
Expression
Ubiquitous expression in testis (RPKM 12.2), bone marrow (RPKM 9.8) and 25 other tissues See more
Orthologs
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Genomic context

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See PSMD12 in Genome Data Viewer
Location:
17q24.2
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (67337916..67366577, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (68213821..68242480, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (65334032..65362693, complement)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA8 Neighboring gene RNA, 5S ribosomal pseudogene 447 Neighboring gene MPRA-validated peak2951 silencer Neighboring gene MPRA-validated peak2952 silencer Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr17:65323222-65323938 Neighboring gene H3K27ac hESC enhancer GRCh37_chr17:65326873-65327713 Neighboring gene Sharpr-MPRA regulatory region 8649 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12621 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12622 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8869 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:65373203-65373896 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8872 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8873 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8874 Neighboring gene uncharacterized LOC124904047 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8875 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12623 Neighboring gene Sharpr-MPRA regulatory region 1189 Neighboring gene phosphatidylinositol transfer protein cytoplasmic 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:65403298-65404268 Neighboring gene small nucleolar RNA U13

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. A replication study of genome-wide CNV association for hepatic biomarkers identifies nine genes associated with liver function. Kim HY, et al. BMB Rep, 2011 Sep. PMID 21944250
  2. Haploinsufficiency of PSMD12 Causes Proteasome Dysfunction and Subclinical Autoinflammation. Yan K, et al. Arthritis Rheumatol, 2022 Jun. PMID 35080150, Free PMC Article
  3. PSMD12 haploinsufficiency in a neurodevelopmental disorder with autistic features. Khalil R, et al. Am J Med Genet B Neuropsychiatr Genet, 2018 Dec. PMID 30421579, Free PMC Article
  4. PSMD12 promotes the activation of the MEK-ERK pathway by upregulating KIF15 to promote the malignant progression of liver cancer. Zhang H, et al. Cancer Biol Ther, 2022 Dec 31. PMID 36137220, Free PMC Article
  5. PSMD12 promotes breast cancer growth via inhibiting the expression of pro-apoptotic genes. Du X, et al. Biochem Biophys Res Commun, 2020 May 28. PMID 32222279

See all (221) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. PSMD12 promotes non-small cell lung cancer progression through activating the Nrf2/TrxR1 pathway.
    Title: PSMD12 promotes non-small cell lung cancer progression through activating the Nrf2/TrxR1 pathway.
  2. PSMD12 interacts with CDKN3 and facilitates pancreatic cancer progression.
    Title: PSMD12 interacts with CDKN3 and facilitates pancreatic cancer progression.
  3. PSMD12 promotes the activation of the MEK-ERK pathway by upregulating KIF15 to promote the malignant progression of liver cancer.
    Title: PSMD12 promotes the activation of the MEK-ERK pathway by upregulating KIF15 to promote the malignant progression of liver cancer.
  4. Haploinsufficiency of PSMD12 Causes Proteasome Dysfunction and Subclinical Autoinflammation.
    Title: Haploinsufficiency of PSMD12 Causes Proteasome Dysfunction and Subclinical Autoinflammation.
  5. PSMD12 promotes breast cancer growth via inhibiting the expression of pro-apoptotic genes.
    Title: PSMD12 promotes breast cancer growth via inhibiting the expression of pro-apoptotic genes.
  6. We performed WES on six affected siblings from a multiplex family with ID and autistic features. We identified an inherited heterozygous nonsense mutation in PSMD12 (NM_002816: c.367C>T: p.R123X) in the multiplex family and a de novo nonsense mutation in the same gene (NM_002816: c.601C>T: p.R201X) in the simplex family.
    Title: PSMD12 haploinsufficiency in a neurodevelopmental disorder with autistic features.
  7. we identified six de novo genomic deletions and four de novo point mutations in unrelated individuals with intellectual disability, congenital malformations, ophthalmologic anomalies, feeding difficulties, deafness, and subtle dysmorphic facial features
    Title: De Novo Disruption of the Proteasome Regulatory Subunit PSMD12 Causes a Syndromic Neurodevelopmental Disorder.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Stankiewicz-Isidor syndrome
MedGen: C4479599 OMIM: 617516 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 (PSMD12) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed

Protein interactions

Protein Gene Interaction Pubs
Tat tat HIV-1 Tat slightly enhances the activity of the purified 26 S proteasome PubMed
tat Amino acids Lys51, Arg52, and Asp67 of HIV-1 Tat represent the proteasome binding site of Tat, and Tat amino acids 37-72 are necessary for proteasomal interaction and suppression of 11 S regulator-mediated antigen presentation PubMed
tat HIV-1 Tat inhibits the peptidase activity of the 20 S proteasome and interferes with the formation of the 20 S proteasome-11 S regulator complex PubMed
tat HIV-1 Tat binds to the alpha2, alpha4, alpha6, alpha7, beta1, beta2, beta3, beta5, beta6, beta7, LMP7/beta5i, and MECL1/beta2i subunits of the proteasome 20 S core structure and can inhibit cellular proteasome function PubMed
Vif vif HIV-1 Vif binds to the cellular cytidine deaminase APOBEC3G and targets it for degradation through an interaction with the proteasome, thereby inhibiting APOBEC3G mediated restriction of HIV-1 replication PubMed
integrase gag-pol Proteasomal degradation of HIV-1 integrase in mammalian cells occurs by the N-end rule pathway PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC75406

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in proteasome-mediated ubiquitin-dependent protein catabolic process NAS
Non-traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in extracellular exosome HDA PubMed 
located_in extracellular region TAS
Traceable Author Statement
more info
  
located_in ficolin-1-rich granule lumen TAS
Traceable Author Statement
more info
  
located_in membrane HDA PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
  
part_of proteasome accessory complex ISS
Inferred from Sequence or Structural Similarity
more info
  
part_of proteasome complex IDA
Inferred from Direct Assay
more info
 PubMed 
part_of proteasome complex NAS
Non-traceable Author Statement
more info
 PubMed 
part_of proteasome regulatory particle TAS
Traceable Author Statement
more info
 PubMed 
part_of proteasome regulatory particle, lid subcomplex IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in secretory granule lumen TAS
Traceable Author Statement
more info
  

General protein information

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Preferred Names
26S proteasome non-ATPase regulatory subunit 12
Names
26S proteasome regulatory subunit RPN5
26S proteasome regulatory subunit p55
proteasome (prosome, macropain) 26S subunit, non-ATPase, 12

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001316341.2 → NP_001303270.1  26S proteasome non-ATPase regulatory subunit 12 isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AC110921, BC065826, BU616916, DC366628
    UniProtKB/Swiss-Prot
    O00232
    Conserved Domains (1) summary
    COG5071
    Location:3 → 397
    RPN5; 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

  2. NM_002816.5 → NP_002807.1  26S proteasome non-ATPase regulatory subunit 12 isoform 1

    See identical proteins and their annotated locations for NP_002807.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC110921, BC019062, BU616916, DC366628
    Consensus CDS
    CCDS11669.1
    UniProtKB/Swiss-Prot
    A6NP15, O00232, Q53HA2, Q6P053
    UniProtKB/TrEMBL
    A0A0S2Z489
    Related
    ENSP00000348442.3, ENST00000356126.8
    Conserved Domains (1) summary
    COG5071
    Location:14 → 456
    RPN5; 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

  3. NM_174871.4 → NP_777360.1  26S proteasome non-ATPase regulatory subunit 12 isoform 2

    See identical proteins and their annotated locations for NP_777360.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame coding exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
    Source sequence(s)
    AC110921, AK091198, BU616916
    Consensus CDS
    CCDS11670.1
    UniProtKB/Swiss-Prot
    O00232
    Related
    ENSP00000349667.4, ENST00000357146.4
    Conserved Domains (1) summary
    COG5071
    Location:17 → 436
    RPN5; 26S proteasome regulatory complex component [Posttranslational modification, protein turnover, chaperones]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    67337916..67366577 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047436440.1 → XP_047292396.1  26S proteasome non-ATPase regulatory subunit 12 isoform X1

    UniProtKB/TrEMBL
    A0A0S2Z476

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    68213821..68242480 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316724.1 → XP_054172699.1  26S proteasome non-ATPase regulatory subunit 12 isoform X1

    UniProtKB/TrEMBL
    A0A0S2Z476
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
O00232.3 GenPept UniProtKB/Swiss-Prot:O00232

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