POMP

gene
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Also known as HSPC014UMP1

Summary

POMP (proteasome maturation protein, HGNC:20330) is a protein-coding gene on chromosome 13q12.3, encoding Proteasome maturation protein (Q9Y244). Molecular chaperone essential for the assembly of standard proteasomes and immunoproteasomes.

The protein encoded by this gene is a molecular chaperone that binds 20S preproteasome components and is essential for 20S proteasome formation. The 20S proteasome is the proteolytically active component of the 26S proteasome complex. The encoded protein is degraded before the maturation of the 20S proteasome is complete. A variant in the 5’ UTR of this gene has been associated with KLICK syndrome, a rare skin disorder.

Source: NCBI Gene 51371 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): keratosis linearis-ichthyosis congenita-sclerosing keratoderma syndrome (Strong, GenCC) — +1 more curated relationship
  • Clinical variants (ClinVar): 158 total — 4 pathogenic, 1 likely-pathogenic
  • MANE Select transcript: NM_015932

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:20330
Approved symbolPOMP
Nameproteasome maturation protein
Location13q12.3
Locus typegene with protein product
StatusApproved
AliasesHSPC014, UMP1
Ensembl geneENSG00000132963
Ensembl biotypeprotein_coding
OMIM613386
Entrez51371

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 13 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000380842, ENST00000460403, ENST00000697661, ENST00000697662, ENST00000697663, ENST00000697716, ENST00000697717, ENST00000697718, ENST00000697719, ENST00000697720, ENST00000697721, ENST00000697722, ENST00000883661, ENST00000883662, ENST00000928922

RefSeq mRNA: 1 — MANE Select: NM_015932 NM_015932

CCDS: CCDS9331

Canonical transcript exons

ENST00000380842 — 6 exons

ExonStartEnd
ENSE000035773172866241028662507
ENSE000036766382867233928672432
ENSE000039715012867803528678959
ENSE000039715042866450928664569
ENSE000039715062865913028659187
ENSE000039715102866847328668574

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 99.43.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 137.7309 / max 3368.2890, expressed in 1826 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
134581137.73091826

Top tissues by expression

288 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
heart right ventricleUBERON:000208099.43gold quality
biceps brachiiUBERON:000150798.94gold quality
mucosa of sigmoid colonUBERON:000499398.90gold quality
corpus epididymisUBERON:000435998.86gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450298.76gold quality
colonic mucosaUBERON:000031798.72gold quality
oral cavityUBERON:000016798.68gold quality
adult organismUBERON:000702398.67gold quality
male germ cellCL:000001598.63gold quality
spermCL:000001998.60gold quality
upper leg skinUBERON:000426298.57gold quality
skeletal muscle tissue of rectus abdominisUBERON:000451198.57gold quality
tendon of biceps brachiiUBERON:000818898.57gold quality
cauda epididymisUBERON:000436098.56gold quality
diaphragmUBERON:000110398.54gold quality
skin of hipUBERON:000155498.53gold quality
trabecular bone tissueUBERON:000248398.48gold quality
deciduaUBERON:000245098.47gold quality
medial globus pallidusUBERON:000247798.45gold quality
triceps brachiiUBERON:000150998.41gold quality
superficial temporal arteryUBERON:000161498.41gold quality
caput epididymisUBERON:000435898.37gold quality
pigmented layer of retinaUBERON:000178298.35gold quality
substantia nigra pars compactaUBERON:000196598.31gold quality
gluteal muscleUBERON:000200098.29gold quality
substantia nigra pars reticulataUBERON:000196698.27gold quality
body of tongueUBERON:001187698.27gold quality
globus pallidusUBERON:000187598.24gold quality
pericardiumUBERON:000240798.24gold quality
type B pancreatic cellCL:000016998.19gold quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 4.

ExperimentMarker?Max mean expression
E-MTAB-8142yes126.97
E-CURD-46yes20.16
E-MTAB-5061yes5.87
E-MTAB-6819no1714.58
E-MTAB-8271no1408.89
E-MTAB-8559no1338.29
E-MTAB-10596no1205.78
E-MTAB-7052no623.79
E-MTAB-6911no556.36
E-HCAD-30no243.58
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

52 targeting POMP, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-5011-5P100.0083.465820
HSA-MIR-5692B100.0071.322622
HSA-MIR-5692C100.0071.322622
HSA-MIR-186-5P99.9970.833707
HSA-MIR-477599.9875.006394
HSA-MIR-302C-5P99.9772.563642
HSA-MIR-590-3P99.9674.346478
HSA-MIR-1250-3P99.9670.044038
HSA-MIR-365899.9673.874379
HSA-MIR-101-3P99.9475.032230
HSA-MIR-144-3P99.9473.982698
HSA-MIR-130599.9171.433443
HSA-MIR-374A-5P99.9071.342923
HSA-MIR-374B-5P99.9069.982734
HSA-MIR-153-5P99.8973.866317
HSA-MIR-5003-3P99.8569.292517
HSA-MIR-132399.8369.892471
HSA-MIR-520F-3P99.8271.321216
HSA-MIR-4766-5P99.7569.232662
HSA-MIR-548O-3P99.7469.302228
HSA-MIR-365999.7067.97694
HSA-MIR-33A-3P99.7070.273362
HSA-MIR-6887-3P99.6667.831778
HSA-MIR-545-5P99.6670.182308
HSA-MIR-452-5P99.6569.631762
HSA-MIR-4676-3P99.6569.311733
HSA-MIR-892C-3P99.6569.381745
HSA-MIR-3177-5P99.6570.381174
HSA-MIR-561-3P99.6470.903647

Literature-anchored findings (GeneRIF, showing 13)

  • POMP/proteassemblin/hUmp1 may be tetramerised and is localized to the cytoplasm and the nucleus (PMID:16624403)
  • Data show that POMP facilitates the main steps in 20S core complex formation at the ER to coordinate the assembly process and to provide cells with freshly formed proteasomes at their site of function. (PMID:17948026)
  • A single-nucleotide deletion in the POMP 5’ UTR causes a transcriptional switch and altered epidermal proteasome distribution in KLICK genodermatosis. (PMID:20226437)
  • KLICK is caused by reduced levels of POMP, leading to proteasome insufficiency in differentiating keratinocytes (PMID:22235297)
  • Single-nucleotide polymorphisms in POMP gene is associated with breast cancer risk after menopausal hormone replacement therapy. (PMID:24080446)
  • microRNA-101 (miR-101) targets the proteasome maturation protein POMP, leading to impaired proteasome assembly and activity, and resulting in accumulation of p53 and cyclin-dependent kinase inhibitors, cell cycle arrest, and apoptosis. (PMID:26145175)
  • studies validate a role for the NRF2/POMP axis in bortezomib resistance and identify NRF2 and POMP as potentially attractive targets for chemosensitization to this proteasome inhibitor (PMID:26483548)
  • MCM3AP and POMP Mutations Cause a DNA-Repair and DNA-Damage-Signaling Defect in an Immunodeficient Child (PMID:26615982)
  • POMP is overexpressed and participates in the increase of proteasome assembly and activity in psoriatic skin. (PMID:28728908)
  • POMP-related autoinflammation and immune dysregulation disease (PRAID) discovered in two unrelated individuals with a unique constellation of early-onset combined immunodeficiency, inflammatory neutrophilic dermatosis, and autoimmunity, is reported. (PMID:29805043)
  • The A alleles of SEMA6A and POMP genes are likely the risk factors of disease development in Georgians. (PMID:31687947)
  • NRF3-POMP-20S Proteasome Assembly Axis Promotes Cancer Development via Ubiquitin-Independent Proteolysis of p53 and Retinoblastoma Protein. (PMID:32123008)
  • KLICK Syndrome Linked to a POMP Mutation Has Features Suggestive of an Autoinflammatory Keratinization Disease. (PMID:32425927)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriopompENSDARG00000032296
mus_musculusPompENSMUSG00000029649
rattus_norvegicusPompENSRNOG00000049229
drosophila_melanogasterPompFBGN0032884

Protein

Protein identifiers

Proteasome maturation proteinQ9Y244 (reviewed: Q9Y244)

Alternative names: Proteassemblin, Protein UMP1 homolog, Voltage-gated K channel beta subunit 4.1

All UniProt accessions (4): A0A1W2PS02, A0A8V8TLM3, A0A8V8TMM8, Q9Y244

UniProt curated annotations — full annotation on UniProt →

Function. Molecular chaperone essential for the assembly of standard proteasomes and immunoproteasomes. Degraded after completion of proteasome maturation. Mediates the association of 20S preproteasome with the endoplasmic reticulum.

Subunit / interactions. Constituent of preproteasomes, but not of mature 20S proteasomes. Within the preproteasome, may directly interact with PSMB1/beta6, PSMB4/beta7, PSMB5/beta5, PSMB6/beta1 and PSMB9/beta1i. Interaction with PSMB8/beta5i has been observed in PubMed:10973495, but not in PubMed:10926487. Forms tetramers.

Subcellular location. Cytoplasm. Cytosol. Nucleus. Microsome membrane.

Tissue specificity. Strongly expressed from the basal layer to the granular layer of healthy epidermis, whereas in KLICK patients there is a gradual decrease of expression toward the granular layer.

Disease relevance. Keratosis linearis with ichthyosis congenita and sclerosing keratoderma (KLICK) [MIM:601952] A keratinizing disorder characterized by ichthyosis, palmoplantar keratoderma with constricting bands around fingers, flexural deformities of fingers and keratotic papules in a linear distribution on the flexural side of large joints. Histological examination of the skin of affected individuals shows hypertrophy and hyperplasia of the spinous, granular and horny epidermal layer. The disease is caused by variants affecting the gene represented in this entry. Proteasome-associated autoinflammatory syndrome 2 (PRAAS2) [MIM:618048] An autosomal dominant autoinflammatory disorder characterized by onset in early infancy and severe inflammatory neutrophilic dermatitis, autoimmunity, and variable immunodeficiency. The disease is caused by variants affecting the gene represented in this entry.

Induction. By IFNG/IFN-gamma.

Similarity. Belongs to the POMP/UMP1 family.

RefSeq proteins (1): NP_057016* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR008012Ump1Family

Pfam: PF05348

UniProt features (15 total): helix 7, strand 3, turn 2, chain 1, short sequence motif 1, cross-link 1

Structure

Experimental structures (PDB)

11 structures.

PDBMethodResolution (Å)
8QYLELECTRON MICROSCOPY2.67
8QYJELECTRON MICROSCOPY2.73
8QYMELECTRON MICROSCOPY2.73
8TM6ELECTRON MICROSCOPY2.8
8QYNELECTRON MICROSCOPY2.88
8YIXELECTRON MICROSCOPY2.91
8QZ9ELECTRON MICROSCOPY2.95
8TM4ELECTRON MICROSCOPY3
8TM5ELECTRON MICROSCOPY3
8YIYELECTRON MICROSCOPY3.41
8QYSELECTRON MICROSCOPY3.89

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9Y244-F181.760.43

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 39

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-9907900Proteasome assembly

MSigDB gene sets: 282 (showing top): KEGG_PROTEASOME, STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, GOBP_PROTEASOME_ASSEMBLY, ONKEN_UVEAL_MELANOMA_UP, GGAANCGGAANY_UNKNOWN, GNF2_XRCC5, ELK1_01, P300_01, NRF2_01, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, GRADE_COLON_AND_RECTAL_CANCER_UP, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN, NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP, GOCC_NUCLEAR_SPECK, GOCC_NUCLEAR_BODY

GO Biological Process (1): proteasome assembly (GO:0043248)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (6): nucleus (GO:0005634), cytoplasm (GO:0005737), cytosol (GO:0005829), nuclear speck (GO:0016607), endoplasmic reticulum (GO:0005783), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Post-translational protein modification1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
intracellular membrane-bounded organelle2
cytoplasm2
protein-containing complex assembly1
binding1
intracellular anatomical structure1
nuclear ribonucleoprotein granule1
endomembrane system1

Protein interactions and networks

STRING

1298 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
POMPPSMB8P28062901
POMPPSMA3P25788882
POMPPSMB9P28065876
POMPPSMB1P20618869
POMPPSMA1P25786867
POMPPSMA4P25789861
POMPPSMG1O95456849
POMPPSMG3Q9BT73788
POMPPSMG4Q5JS54787
POMPPSMA7O14818766
POMPECPASQ5VYK3726
POMPPSME4Q14997722
POMPPSMB4P28070718
POMPPSMG2Q969U7717
POMPPSMB5P28074710

IntAct

141 interactions, top by confidence:

ABTypeScore
PSMA1PSMA7psi-mi:“MI:0914”(association)0.950
PSMA1PSMA7psi-mi:“MI:2364”(proximity)0.950
PSMA7PSMA1psi-mi:“MI:0914”(association)0.950
POMPPSMB7psi-mi:“MI:0915”(physical association)0.910
PSMB7POMPpsi-mi:“MI:0915”(physical association)0.910
POMPPSMB3psi-mi:“MI:0915”(physical association)0.860
POMPPSMB1psi-mi:“MI:0915”(physical association)0.860
PSMB3POMPpsi-mi:“MI:0915”(physical association)0.860
PSMA2PSMA7psi-mi:“MI:0914”(association)0.850
PSMG2PSMG1psi-mi:“MI:0914”(association)0.850
PSMA6PSMA7psi-mi:“MI:0914”(association)0.850
POMPPSMB2psi-mi:“MI:0915”(physical association)0.810
PSMA5PSMA7psi-mi:“MI:0914”(association)0.800
PSMB7PSMA7psi-mi:“MI:0914”(association)0.790
PSMB2PSMA7psi-mi:“MI:0914”(association)0.790
PSMB3PSMA7psi-mi:“MI:0914”(association)0.770
PSMB5POMPpsi-mi:“MI:0915”(physical association)0.760
PSMB6POMPpsi-mi:“MI:0915”(physical association)0.760
POMPPSMB6psi-mi:“MI:0915”(physical association)0.760
POMPPSMB4psi-mi:“MI:0915”(physical association)0.750

BioGRID (157): POMP (Affinity Capture-MS), POMP (Affinity Capture-MS), POMP (Affinity Capture-MS), POMP (Affinity Capture-MS), POMP (Affinity Capture-MS), POMP (Affinity Capture-MS), POMP (Affinity Capture-MS), POMP (Co-fractionation), PSMA4 (Co-fractionation), PSMA5 (Co-fractionation), PSMB7 (Co-fractionation), PSMC2 (Co-fractionation), PSMC3 (Co-fractionation), PSMD2 (Co-fractionation), POMP (Affinity Capture-MS)

ESM2 similar proteins: A0A0G3VTN5, A0A0P0XBU0, A0A2K1L2D9, A2X0Q6, A3A2Z8, A9XMT4, B8YIE8, B9F1C0, C7IW64, F4I096, F4J7T2, F4J7T3, F4JTS8, F4K1J4, O65685, P0C1C7, P0C945, P0CB21, P92973, Q2LAE1, Q53HY2, Q5E9A0, Q5R9L9, Q5Z8V7, Q657D6, Q689G6, Q6IRT3, Q703I1, Q766Z3, Q86XD8, Q8LFU0, Q8S9L0, Q93WK5, Q94FL9, Q94JW8, Q9CAA9, Q9CQT5, Q9FRG8, Q9FZK0, Q9LE42

Diamond homologs: Q0DWQ7, Q3SZV5, Q5R9L9, Q9CQT5, Q9Y244

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 71 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Antigen processing: Ub, ATP-independent proteasomal degradation16179.1×4e-34
Regulation of activated PAK-2p34 by proteasome mediated degradation19103.8×4e-34
Proteasome assembly25100.0×4e-44
Cross-presentation of soluble exogenous antigens (endosomes)2099.5×8e-35
Vpu mediated degradation of CD41998.9×1e-33
Autodegradation of the E3 ubiquitin ligase COP11998.9×1e-33
Ubiquitin-dependent degradation of Cyclin D1998.9×1e-33
AUF1 (hnRNP D0) binds and destabilizes mRNA2097.4×8e-35

GO biological processes:

GO termPartnersFoldFDR
proteasome-mediated ubiquitin-dependent protein catabolic process2321.4×8e-23

Disease & clinical

Clinical variants and AI predictions

ClinVar

158 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic4
Likely pathogenic1
Uncertain significance77
Likely benign57
Benign10

Top pathogenic / likely-pathogenic (5)

Variant IDHGVSClassification
116NC_000013.11:g.28659090delPathogenic
522801NM_015932.6(POMP):c.334_335del (p.Ile112fs)Pathogenic
548959NM_015932.6(POMP):c.340_344dup (p.Glu115fs)Pathogenic
548960NM_015932.6(POMP):c.342_348delinsACC (p.Phe114fs)Pathogenic
546726NM_015932.6(POMP):c.326dup (p.Asp109fs)Likely pathogenic

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

925 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
13:28668524:G:CG72R0.990
13:28668563:G:CA85P0.985
13:28668525:G:TG72V0.982
13:28668510:T:CL67P0.981
13:28668534:C:AA75D0.981
13:28664550:T:AL48H0.979
13:28668540:T:CL77P0.979
13:28668525:G:AG72D0.978
13:28664550:T:CL48P0.975
13:28668554:G:AE82K0.970
13:28672427:T:CL118P0.969
13:28668549:A:CQ80P0.967
13:28664545:T:AH46Q0.966
13:28664545:T:GH46Q0.966
13:28668524:G:TG72C0.966
13:28672354:T:CF94L0.966
13:28672356:T:AF94L0.966
13:28672356:T:GF94L0.966
13:28672414:T:CF114L0.965
13:28672416:T:AF114L0.965
13:28672416:T:GF114L0.965
13:28672388:T:CL105S0.963
13:28678080:A:TE135V0.960
13:28668544:A:CK78N0.957
13:28668544:A:TK78N0.957
13:28672385:T:AV104D0.957
13:28672394:G:TG107V0.956
13:28664544:A:GH46R0.955
13:28668525:G:CG72A0.953
13:28668522:A:CQ71P0.952

dbSNP variants (sampled 300 via entrez): RS1000043810 (13:28676907 G>A), RS1000417646 (13:28658975 A>C), RS1000640320 (13:28678479 A>G), RS1000821114 (13:28672627 G>A), RS1000896658 (13:28673966 T>G), RS1000994170 (13:28678768 G>A,T), RS1001107754 (13:28672297 T>G), RS1001180573 (13:28662222 A>G), RS1001488698 (13:28671821 A>G), RS1001489626 (13:28659501 G>A,C), RS1001519989 (13:28671520 C>T), RS1001611240 (13:28674717 G>A), RS1001666273 (13:28667874 G>T), RS1001717206 (13:28667705 C>T), RS1001998439 (13:28666843 C>G,T)

Disease associations

OMIM: gene MIM:613386 | disease phenotypes: MIM:601952, MIM:618048

GenCC curated gene-disease

DiseaseClassificationInheritance
keratosis linearis-ichthyosis congenita-sclerosing keratoderma syndromeStrongAutosomal recessive
proteasome-associated autoinflammatory syndrome 2StrongAutosomal dominant

Mondo (2): keratosis linearis-ichthyosis congenita-sclerosing keratoderma syndrome (MONDO:0011169), proteasome-associated autoinflammatory syndrome 2 (MONDO:0054700)

Orphanet (1): Keratosis linearis-ichthyosis congenita-sclerosing keratoderma syndrome (Orphanet:281201)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

DescriptorNameTree numbers
C566600Keratosis Linearis with Ichthyosis Congenita and Sclerosing Keratoderma (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

31 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects cotreatment, decreases expression, increases abundance, increases expression6
Valproic Acidaffects expression, increases expression2
Cadmium Chlorideincreases abundance, increases expression2
Particulate Matterdecreases expression, increases abundance, increases expression2
dicrotophosdecreases expression1
triphenyl phosphateaffects expression1
bisphenol Adecreases expression1
lead acetateaffects cotreatment, decreases expression1
beta-lapachoneincreases expression1
arseniteaffects binding, increases reaction1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
cupric chlorideincreases expression1
perfluorodecanoic acidincreases expression1
chloropicrinincreases expression1
jinfukangdecreases expression1
Vorinostatincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicaffects cotreatment, increases abundance, increases expression1
Benzo(a)pyreneincreases methylation1
Cadmiumincreases abundance, increases expression1
Doxorubicinincreases expression1
Manganeseincreases expression, affects cotreatment, increases abundance1
Smokedecreases expression1
Thiramincreases expression1
Tobacco Smoke Pollutionincreases expression1
Cyclosporineincreases expression1
Aflatoxin B1increases methylation1
Okadaic Acidincreases expression1
Copper Sulfateincreases expression1
Lactic Aciddecreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.