PXMP4

Summary

PXMP4 (peroxisomal membrane protein 4, HGNC:15920) is a protein-coding gene on chromosome 20q11.22, encoding Peroxisomal membrane protein 4 (Q9Y6I8).

Predicted to act upstream of or within ether lipid metabolic process. Located in peroxisomal membrane.

Source: NCBI Gene 11264 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 44 total
• Druggable target: yes
• MANE Select transcript: NM_007238

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:15920
Approved symbol	PXMP4
Name	peroxisomal membrane protein 4
Location	20q11.22
Locus type	gene with protein product
Status	Approved
Aliases	PMP24
Ensembl gene	ENSG00000101417
Ensembl biotype	protein_coding
OMIM	616397
Entrez	11264

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000217398, ENST00000344022, ENST00000409299, ENST00000945198

RefSeq mRNA: 2 — MANE Select: NM_007238 NM_007238, NM_183397

CCDS: CCDS13225, CCDS13226

Canonical transcript exons

ENST00000409299 — 4 exons

Exon	Start	End
ENSE00000661350	33714674	33714736
ENSE00000860063	33710555	33710753
ENSE00001587941	33702758	33707969
ENSE00001925420	33720095	33720310

Expression profiles

Bgee: expression breadth ubiquitous, 230 present calls, max score 84.30.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 10.9655 / max 147.9150, expressed in 1684 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
186973	10.2506	1671
186971	0.4502	192
186972	0.2647	130

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper leg skin	UBERON:0004262	84.30	gold quality
right adrenal gland cortex	UBERON:0035827	82.00	gold quality
right adrenal gland	UBERON:0001233	81.90	gold quality
type B pancreatic cell	CL:0000169	81.67	gold quality
olfactory bulb	UBERON:0002264	81.55	gold quality
pancreatic ductal cell	CL:0002079	81.51	silver quality
cervix squamous epithelium	UBERON:0006922	81.27	silver quality
mammalian vulva	UBERON:0000997	81.07	gold quality
left adrenal gland	UBERON:0001234	80.61	gold quality
left adrenal gland cortex	UBERON:0035825	80.21	gold quality
hindlimb stylopod muscle	UBERON:0004252	79.84	gold quality
adrenal gland	UBERON:0002369	79.27	gold quality
adrenal cortex	UBERON:0001235	79.21	gold quality
cortical plate	UBERON:0005343	78.32	gold quality
parotid gland	UBERON:0001831	78.21	silver quality
ileal mucosa	UBERON:0000331	77.95	silver quality
mucosa of transverse colon	UBERON:0004991	77.93	gold quality
lower lobe of lung	UBERON:0008949	77.90	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.87	gold quality
muscle of leg	UBERON:0001383	77.10	gold quality
stromal cell of endometrium	CL:0002255	76.86	gold quality
skin of abdomen	UBERON:0001416	76.58	gold quality
gastrocnemius	UBERON:0001388	76.50	gold quality
smooth muscle tissue	UBERON:0001135	76.43	gold quality
prefrontal cortex	UBERON:0000451	76.25	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	76.14	gold quality
squamous epithelium	UBERON:0006914	76.08	gold quality
skin of leg	UBERON:0001511	76.01	gold quality
zone of skin	UBERON:0000014	75.99	gold quality
saliva-secreting gland	UBERON:0001044	75.96	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

151 targeting PXMP4, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-4692	100.00	67.32	2066
HSA-MIR-4682	100.00	68.89	1258
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-4534	99.99	66.58	1907
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-150-5P	99.99	66.69	1976
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-4514	99.99	67.10	1870
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-4715-3P	99.98	66.03	670
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-6778-3P	99.96	67.29	2693
HSA-MIR-4725-3P	99.96	69.53	2520
HSA-MIR-6780B-5P	99.96	69.60	2562
HSA-MIR-6825-5P	99.96	69.81	3431
HSA-MIR-4267	99.96	66.53	2368
HSA-MIR-8082	99.95	67.27	1170
HSA-MIR-497-5P	99.92	71.83	2674
HSA-MIR-329-3P	99.91	66.56	1234
HSA-MIR-362-3P	99.91	66.38	1267

Literature-anchored findings (GeneRIF, showing 2)

• PXMP4 promotes gastric cancer cell epithelial-mesenchymal transition via the PI3K/AKT signaling pathway. (PMID:38401002)
• High Expression of PXMP4 in Hepatocellular Carcinoma Tissues. (PMID:38415547)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	pxmp4	ENSDARG00000114885
mus_musculus	Pxmp4	ENSMUSG00000000876
rattus_norvegicus	Pxmp4	ENSRNOG00000016975
caenorhabditis_elegans		WBGENE00017574

Protein

Protein identifiers

Peroxisomal membrane protein 4 — Q9Y6I8 (reviewed: Q9Y6I8)

Alternative names: 24 kDa peroxisomal intrinsic membrane protein

All UniProt accessions (2): Q9Y6I8, B4DWH1

UniProt curated annotations — full annotation on UniProt →

Subunit / interactions. Interacts with PEX19.

Subcellular location. Peroxisome membrane.

Tissue specificity. Expressed in normal prostate epithelial cells, and androgen-sensitive prostate adenocarcinoma cells. Not expressed in androgen-insensitive prostate adenocarcinoma cells.

Miscellaneous. Hypermethylation-mediated silencing of PXMP4 may be involved in prostate carcinogenesis. PXMP4 undergoes hypermethylation and silencing during the transition of prostate adenocarcinoma cells from androgen dependence to androgen independence.

Similarity. Belongs to the peroxisomal membrane protein PXMP2/4 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9Y6I8-1	1	yes
Q9Y6I8-2	2

RefSeq proteins (2): NP_009169, NP_899634 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR019531	Pmp4	Family

Pfam: PF02466

UniProt features (8 total): transmembrane region 2, glycosylation site 2, splice variant 2, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9Y6I8-F1	91.79	0.77

Functional residue map

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

Glycosylation sites (2): 57, 206

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

ID	Pathway
R-HSA-9603798	Class I peroxisomal membrane protein import

MSigDB gene sets: 124 (showing top): GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_UP, GSE18804_SPLEEN_MACROPHAGE_VS_COLON_TUMORAL_MACROPHAGE_UP, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, LI_PROSTATE_CANCER_EPIGENETIC, PATIL_LIVER_CANCER, GOBP_LIPID_METABOLIC_PROCESS, GOCC_MICROBODY_MEMBRANE, chr20q11, SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN, MODULE_342, GOCC_MICROBODY, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, STEIN_ESRRA_TARGETS_UP, GSE13762_CTRL_VS_125_VITAMIND_DAY5_DC_DN, TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP

GO Biological Process (1): ether lipid metabolic process (GO:0046485)

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

GO Cellular Component (4): peroxisome (GO:0005777), peroxisomal membrane (GO:0005778), cytosol (GO:0005829), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

Category	Pathways
Protein localization	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
lipid metabolic process	1
binding	1
microbody	1
peroxisome	1
microbody membrane	1
cytoplasm	1

Protein interactions and networks

STRING

690 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PXMP4	PEX19	P40855	738
PXMP4	TMEM135	Q86UB9	690
PXMP4	PEX11A	O75192	642
PXMP4	PEX11B	O96011	642
PXMP4	PXMP2	Q9NR77	571
PXMP4	TIMM17A	Q99595	534
PXMP4	SLC25A17	O43808	530
PXMP4	PEX11G	Q96HA9	524
PXMP4	ZNF341	Q9BYN7	521
PXMP4	FAM151B	Q6UXP7	513
PXMP4	PEX16	Q9Y5Y5	510
PXMP4	NUDT19	A8MXV4	490
PXMP4	BTBD8	Q5XKL5	485
PXMP4	C20orf144	Q9BQM9	472
PXMP4	ACOT8	O14734	469

IntAct

11 interactions, top by confidence:

A	B	Type	Score
SLC6A8	ILVBL	psi-mi:“MI:0914”(association)	0.530
PXMP4	PGAM2	psi-mi:“MI:0915”(physical association)	0.400
PXMP4	PEX19	psi-mi:“MI:0915”(physical association)	0.400
NS3	C15orf61	psi-mi:“MI:0914”(association)	0.350
TNNC2	PLEKHG3	psi-mi:“MI:0914”(association)	0.350
SLC12A9	PGRMC1	psi-mi:“MI:0914”(association)	0.350
SLC1A1	SCD	psi-mi:“MI:0914”(association)	0.350
SLC39A12	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC39A7	ESYT2	psi-mi:“MI:0914”(association)	0.350
SLC39A8	CEBPZOS	psi-mi:“MI:0914”(association)	0.350
SLC4A5	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (10): PXMP4 (Affinity Capture-MS), PGAM2 (Affinity Capture-MS), PXMP4 (Affinity Capture-MS), PXMP4 (Affinity Capture-MS), PXMP4 (Affinity Capture-MS), PXMP4 (Affinity Capture-MS), PXMP4 (Affinity Capture-MS), PXMP4 (Affinity Capture-MS), PXMP4 (Affinity Capture-MS), PXMP4 (Affinity Capture-Western)

ESM2 similar proteins: A2RVP7, A5PJL1, A6QP55, F4I8Q7, P0CR88, P0CR89, P59382, P61803, P61804, P61805, P61806, Q1L9A2, Q29036, Q2KIK2, Q2KIY1, Q2QL34, Q32LG5, Q38820, Q3ZBE6, Q3ZBX1, Q5E9C2, Q5EA43, Q5RD16, Q5U4F4, Q5XF36, Q5XI60, Q5XK94, Q641S2, Q68FV1, Q6DIY8, Q6GQ39, Q6INU6, Q6NYK8, Q7T2P6, Q7ZVP8, Q86UB9, Q8IN78, Q8R2R1, Q91V61, Q925N2

Diamond homologs: A5PJL1, P59382, Q9JJW0, Q9Y6I8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	32
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

781 predictions. Top by Δscore:

Variant	Effect	Δscore
20:33707970:C:CC	acceptor_gain	1.0000
20:33714732:CATAG:C	acceptor_gain	1.0000
20:33714733:ATAGC:A	acceptor_loss	1.0000
20:33714734:TAG:T	acceptor_gain	1.0000
20:33714735:AG:A	acceptor_gain	1.0000
20:33714735:AGCTG:A	acceptor_loss	1.0000
20:33714736:GCTG:G	acceptor_loss	1.0000
20:33714737:C:CC	acceptor_gain	1.0000
20:33714737:C:T	acceptor_loss	1.0000
20:33714738:T:A	acceptor_loss	1.0000
20:33720093:A:AC	donor_gain	1.0000
20:33720094:C:CC	donor_gain	1.0000
20:33720094:CA:C	donor_gain	1.0000
20:33720094:CACAG:C	donor_gain	1.0000
20:33707966:TGAT:T	acceptor_gain	0.9900
20:33707967:GATC:G	acceptor_loss	0.9900
20:33707969:TC:T	acceptor_loss	0.9900
20:33707970:CT:C	acceptor_loss	0.9900
20:33707971:T:C	acceptor_loss	0.9900
20:33710549:CTTTA:C	donor_loss	0.9900
20:33710550:TTTAC:T	donor_loss	0.9900
20:33710551:TTACC:T	donor_loss	0.9900
20:33710552:TACCT:T	donor_loss	0.9900
20:33710553:ACCTG:A	donor_loss	0.9900
20:33710554:CCTG:C	donor_loss	0.9900
20:33710554:CCTGG:C	donor_gain	0.9900
20:33714668:GTGTA:G	donor_loss	0.9900
20:33714669:TGTAC:T	donor_loss	0.9900
20:33714670:GTACC:G	donor_loss	0.9900
20:33714671:TACCT:T	donor_loss	0.9900

AlphaMissense

1359 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
20:33714685:G:C	F55L	0.989
20:33714685:G:T	F55L	0.989
20:33714687:A:G	F55L	0.989
20:33720115:C:A	K31N	0.987
20:33720115:C:G	K31N	0.987
20:33710687:A:C	F81L	0.983
20:33710687:A:T	F81L	0.983
20:33710689:A:G	F81L	0.983
20:33707759:A:G	W196R	0.982
20:33707759:A:T	W196R	0.982
20:33707855:A:G	W164R	0.982
20:33707855:A:T	W164R	0.982
20:33720114:C:G	G32R	0.979
20:33707766:G:C	S193R	0.978
20:33707766:G:T	S193R	0.978
20:33707768:T:G	S193R	0.978
20:33707832:A:C	F171L	0.978
20:33707832:A:T	F171L	0.978
20:33707834:A:G	F171L	0.978
20:33707852:C:G	G165R	0.978
20:33707852:C:T	G165R	0.978
20:33707948:G:T	R133S	0.978
20:33710582:A:C	F116L	0.975
20:33710582:A:T	F116L	0.975
20:33710584:A:G	F116L	0.975
20:33720107:C:G	R34P	0.975
20:33710730:A:T	I67K	0.973
20:33714708:C:G	A48P	0.972
20:33720102:C:A	G36W	0.972
20:33707800:A:G	L182P	0.971

dbSNP variants (sampled 300 via entrez): RS1000097820 (20:33706079 C>T), RS1000188738 (20:33703129 G>T), RS1000293581 (20:33707807 G>A), RS1000341684 (20:33722269 G>A), RS1000370602 (20:33709464 T>C), RS1000492832 (20:33713572 C>T), RS1000834919 (20:33714812 T>C), RS1000887252 (20:33715163 T>C), RS1001053014 (20:33721014 C>T), RS1001172216 (20:33717312 G>C), RS1001496220 (20:33717677 G>A,T), RS1001550242 (20:33717963 C>A,T), RS1001804753 (20:33704125 G>T), RS1001858781 (20:33704307 A>G), RS1002038272 (20:33711387 G>A)

Disease associations

OMIM: gene MIM:616397 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST001956_73	Height	1.000000e-14
GCST002647_168	Height	8.000000e-38
GCST003264_16	Post bronchodilator FEV1/FVC ratio	1.000000e-06
GCST006940_39	Neurociticism	1.000000e-08
GCST006948_54	Feeling nervous	3.000000e-10
GCST012227_1369	Hip circumference adjusted for BMI	2.000000e-08
GCST90000025_640	Appendicular lean mass	2.000000e-63

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004713	FEV/FVC ratio
EFO:0007660	neuroticism measurement
EFO:0009597	feeling nervous measurement
EFO:0008039	BMI-adjusted hip circumference
EFO:0004980	appendicular lean mass

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL6067435 (SINGLE PROTEIN)

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

ChEMBL bioactivities

2 potent at pChembl≥5 of 2 total, top 2 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChembl	Type	Value	Unit	Molecule
5.64	Kd	2301	nM	CHEMBL5653589
5.64	ED50	2301	nM	CHEMBL5653589

PubChem BioAssay actives

1 with measured affinity, of 2 total; 1 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

Compound	Assay	Type	Value	Unit
4-methyl-3-[(2-methyl-6-pyridin-3-ylpyrazolo[3,4-d]pyrimidin-4-yl)amino]-N-[3-(trifluoromethyl)phenyl]benzamide	2149156: Binding affinity to human PXMP4 incubated for 45 mins by Kinobead based pull down assay	kd	2.3009	uM

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases abundance, increases expression	3
Nickel	decreases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
aristolochic acid I	increases expression	1
GSK-J4	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
pirinixic acid	increases activity, increases expression, affects binding	1
bisphenol A	affects cotreatment, increases expression	1
arsenite	increases methylation	1
butyraldehyde	decreases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
pentanal	decreases expression	1
pinosylvin	increases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	affects binding, increases reaction	1
perfluoro-n-nonanoic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
abrine	decreases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Sunitinib	decreases expression	1
Arsenic	decreases expression, increases abundance	1
Benzo(a)pyrene	increases methylation	1
Cisplatin	increases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Indomethacin	affects cotreatment, increases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 binding

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL5652198	Binding	Binding affinity to human PXMP4 incubated for 45 mins by Kinobead based pull down assay	NVP-BHG712: Effects of Regioisomers on the Affinity and Selectivity toward the EPHrin Family. — ChemMedChem

Clinical trials (associated diseases)

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