PXMP2

Summary

PXMP2 (peroxisomal membrane protein 2, HGNC:9716) is a protein-coding gene on chromosome 12q24.33, encoding Peroxisomal membrane protein 2 (Q9NR77). Seems to be involved in pore-forming activity and may contribute to the unspecific permeability of the peroxisomal membrane.

Located in peroxisomal membrane. Part of protein-containing complex.

Source: NCBI Gene 5827 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 40 total — 1 pathogenic
• MANE Select transcript: NM_018663

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:9716
Approved symbol	PXMP2
Name	peroxisomal membrane protein 2
Location	12q24.33
Locus type	gene with protein product
Status	Approved
Aliases	PMP22, MPV17L3
Ensembl gene	ENSG00000176894
Ensembl biotype	protein_coding
OMIM	617399
Entrez	5827

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 8 protein_coding, 1 nonsense_mediated_decay

ENST00000317479, ENST00000428960, ENST00000454379, ENST00000539093, ENST00000543589, ENST00000856532, ENST00000856533, ENST00000856534, ENST00000856535

RefSeq mRNA: 1 — MANE Select: NM_018663 NM_018663

CCDS: CCDS9279

Canonical transcript exons

ENST00000317479 — 5 exons

Exon	Start	End
ENSE00001293459	132687587	132687792
ENSE00002230284	132704619	132704985
ENSE00003467180	132701250	132701369
ENSE00003468031	132690263	132690376
ENSE00003715973	132695884	132696046

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 98.68.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.0443 / max 167.0632, expressed in 1767 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
128828	18.0443	1767

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right lobe of liver	UBERON:0001114	98.68	gold quality
liver	UBERON:0002107	98.16	gold quality
mucosa of transverse colon	UBERON:0004991	97.90	gold quality
body of stomach	UBERON:0001161	95.69	gold quality
apex of heart	UBERON:0002098	95.09	gold quality
duodenum	UBERON:0002114	95.09	gold quality
adult mammalian kidney	UBERON:0000082	94.96	gold quality
fundus of stomach	UBERON:0001160	94.62	gold quality
heart left ventricle	UBERON:0002084	94.49	gold quality
stomach	UBERON:0000945	94.45	gold quality
ventricular zone	UBERON:0003053	93.63	gold quality
transverse colon	UBERON:0001157	93.60	gold quality
ganglionic eminence	UBERON:0004023	92.56	gold quality
kidney	UBERON:0002113	92.54	gold quality
heart	UBERON:0000948	92.52	gold quality
gastrocnemius	UBERON:0001388	91.87	gold quality
small intestine Peyer’s patch	UBERON:0003454	91.75	gold quality
rectum	UBERON:0001052	91.72	gold quality
body of pancreas	UBERON:0001150	91.69	gold quality
small intestine	UBERON:0002108	91.57	gold quality
muscle of leg	UBERON:0001383	91.51	gold quality
right atrium auricular region	UBERON:0006631	91.27	gold quality
hindlimb stylopod muscle	UBERON:0004252	91.15	gold quality
skeletal muscle tissue	UBERON:0001134	90.47	gold quality
thoracic aorta	UBERON:0001515	90.41	gold quality
descending thoracic aorta	UBERON:0002345	90.37	gold quality
ascending aorta	UBERON:0001496	90.33	gold quality
intestine	UBERON:0000160	90.17	gold quality
colon	UBERON:0001155	89.80	gold quality
cortex of kidney	UBERON:0001225	89.73	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	8.69

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting PXMP2, 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-153-5P	99.89	73.86	6317
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-20A-3P	99.44	69.10	1575
HSA-MIR-7151-5P	99.37	67.82	613
HSA-MIR-6719-3P	99.29	67.78	1387
HSA-MIR-6804-3P	98.72	64.82	852
HSA-MIR-3622A-3P	97.06	66.43	1000
HSA-MIR-4793-5P	96.88	65.90	872
HSA-MIR-3622B-3P	96.82	66.36	988
HSA-MIR-152-5P	96.42	66.59	960

Literature-anchored findings (GeneRIF, showing 1)

• Authors provide evidence that PXMP2 is not essential for H2O2 permeation across the peroxisomal membrane, neither in control cells nor in cells lacking PEX11B, a peroxisomal membrane-shaping protein whose yeast homologue facilitates the permeation of molecules up to 400Da. (PMID:31129117)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	pxmp2	ENSDARG00000003144
mus_musculus	Pxmp2	ENSMUSG00000029499
rattus_norvegicus	Pxmp2	ENSRNOG00000037446
drosophila_melanogaster	CG7970	FBGN0035252

Paralogs (3): MPV17 (ENSG00000115204), MPV17L (ENSG00000156968), MPV17L2 (ENSG00000254858)

Protein

Protein identifiers

Peroxisomal membrane protein 2 — Q9NR77 (reviewed: Q9NR77)

Alternative names: 22 kDa peroxisomal membrane protein

All UniProt accessions (5): A0A087X249, Q9NR77, F5GXM0, F5GZF7, F5H4N4

UniProt curated annotations — full annotation on UniProt →

Function. Seems to be involved in pore-forming activity and may contribute to the unspecific permeability of the peroxisomal membrane.

Subunit / interactions. Interacts with PEX19 and SIVA1.

Subcellular location. Peroxisome membrane.

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

RefSeq proteins (1): NP_061133* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007248	Mpv17_PMP22	Family

Pfam: PF04117

UniProt features (9 total): topological domain 4, transmembrane region 4, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NR77-F1	85.58	0.51

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-389661	Glyoxylate metabolism and glycine degradation
R-HSA-9603798	Class I peroxisomal membrane protein import

MSigDB gene sets: 757 (showing top): WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN, TGGTGCT_MIR29A_MIR29B_MIR29C, chr17p12, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, BENPORATH_ES_WITH_H3K27ME3, CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN, YAGI_AML_WITH_INV_16_TRANSLOCATION, KAAB_FAILED_HEART_ATRIUM_DN, GNF2_GSTM1, GNF2_HPN, ASTON_MAJOR_DEPRESSIVE_DISORDER_DN, SCHLESINGER_METHYLATED_DE_NOVO_IN_CANCER, GOBP_NEUROGENESIS, KANNAN_TP53_TARGETS_DN, TOMLINS_PROSTATE_CANCER_DN

GO Biological Process (0):

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

GO Cellular Component (6): cytoplasm (GO:0005737), peroxisomal membrane (GO:0005778), cytosol (GO:0005829), membrane (GO:0016020), protein-containing complex (GO:0032991), peroxisome (GO:0005777)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Metabolism of amino acids and derivatives	1
Protein localization	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
binding	1
intracellular anatomical structure	1
peroxisome	1
microbody membrane	1
cytoplasm	1
cellular_component	1
microbody	1

Protein interactions and networks

STRING

1072 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PXMP2	PEX11A	O75192	653
PXMP2	PEX11B	O96011	651
PXMP2	PEX16	Q9Y5Y5	597
PXMP2	PXMP4	Q9Y6I8	571
PXMP2	PEX11G	Q96HA9	549
PXMP2	DAO	P14920	532
PXMP2	ACBD5	Q5T8D3	501
PXMP2	SLC25A17	O43808	489
PXMP2	ALDH3A2	P51648	470
PXMP2	PEX13	Q92968	468
PXMP2	SNX15	Q9NRS6	466
PXMP2	NUDT12	Q9BQG2	459
PXMP2	ABCD1	P33897	458
PXMP2	H3BMD7	H3BMD7	453
PXMP2	HAO1	Q9UJM8	448

IntAct

73 interactions, top by confidence:

A	B	Type	Score
IFT70B	IFT56	psi-mi:“MI:0914”(association)	0.790
PXMP2	PEX19	psi-mi:“MI:0915”(physical association)	0.770
PXMP2	PEX19	psi-mi:“MI:0407”(direct interaction)	0.770
TRDN	TMEM223	psi-mi:“MI:0914”(association)	0.640
MME	TMEM223	psi-mi:“MI:0914”(association)	0.530
SLC15A1	METTL15	psi-mi:“MI:0914”(association)	0.530
SLC39A9	B4GALT5	psi-mi:“MI:0914”(association)	0.530
PEX19	FAM20B	psi-mi:“MI:0914”(association)	0.530
SLC22A16	APBA3	psi-mi:“MI:0914”(association)	0.530
PEX19	MYO1D	psi-mi:“MI:0914”(association)	0.530
PXMP2	SIVA1	psi-mi:“MI:0915”(physical association)	0.510
SIVA1	PXMP2	psi-mi:“MI:0915”(physical association)	0.510
GPC1	SNAP23	psi-mi:“MI:0915”(physical association)	0.400
GPC1	GANAB	psi-mi:“MI:0915”(physical association)	0.400
ERGIC3	TMEM223	psi-mi:“MI:0914”(association)	0.350
TMCO3	POTEF	psi-mi:“MI:0914”(association)	0.350
SLC18A1	LIMK2	psi-mi:“MI:0914”(association)	0.350
FPR2	GPR89A	psi-mi:“MI:0914”(association)	0.350
SLC5A8	GPR89A	psi-mi:“MI:0914”(association)	0.350
SLC6A15	GPR89A	psi-mi:“MI:0914”(association)	0.350
SLC1A1	TNFRSF10B	psi-mi:“MI:0914”(association)	0.350
SLC22A16	AGPAT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (301): KRT40 (Two-hybrid), PXMP2 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS), PXMP2 (Affinity Capture-MS)

ESM2 similar proteins: A6ZV78, A7A285, A8E7G5, B0G159, B3LUQ6, B5VI70, O14142, P0CQ38, P0CQ39, P38857, P40464, P42925, P43617, P53257, Q06563, Q07066, Q10244, Q2KIK2, Q2KIY1, Q2QL34, Q3ZCG2, Q4P9K6, Q4WDZ0, Q54FR4, Q54GD8, Q54XX9, Q54ZX5, Q59Q43, Q5EA43, Q5RD16, Q60SZ2, Q68F62, Q6BMY0, Q6CAW5, Q6CIY7, Q6FXJ3, Q754F0, Q7YWV6, Q86I81, Q925N2

Diamond homologs: O14142, P0CQ38, P0CQ39, P19258, P39210, P42925, Q06563, Q07066, Q08743, Q10244, Q2KIN6, Q2KIY1, Q2TXA2, Q4IPX8, Q4P9K6, Q4WDZ0, Q54XX9, Q54ZX5, Q59Q43, Q5BK62, Q5TZ51, Q60SZ2, Q66GV0, Q6BMY0, Q6CAW5, Q6CIY7, Q6FXJ3, Q754F0, Q7SCY7, Q9NR77, Q54FR4, Q54GD8, Q6DGV7, Q2QL34, Q567V2, Q8VIK2, A5D787, Q6DIY8, Q7YWV6, Q99MS3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 82 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:

Pathway	Partners	Fold	FDR
R-HSA-425393	6	15.0×	2e-04
SLC-mediated transmembrane transport	10	11.4×	3e-06
Transport of small molecules	13	6.3×	9e-06

GO biological processes:

GO term	Partners	Fold	FDR
sodium ion transport	5	17.4×	3e-03
monoatomic ion transport	6	12.0×	3e-03
intracellular calcium ion homeostasis	6	11.2×	3e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	25
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
638102	GRCh37/hg19 12q24.33(chr12:131363916-133777645)x3	Pathogenic

SpliceAI

1558 predictions. Top by Δscore:

Variant	Effect	Δscore
12:132687792:GGTG:G	donor_loss	1.0000
12:132687793:GTGAG:G	donor_loss	1.0000
12:132690261:A:AG	acceptor_gain	1.0000
12:132690262:G:GG	acceptor_gain	1.0000
12:132690262:GTGGC:G	acceptor_gain	1.0000
12:132690375:GG:G	donor_gain	1.0000
12:132690376:GG:G	donor_gain	1.0000
12:132690377:G:GG	donor_gain	1.0000
12:132690377:G:T	donor_loss	1.0000
12:132690378:T:A	donor_loss	1.0000
12:132701244:TTGCA:T	acceptor_loss	1.0000
12:132701245:T:TA	acceptor_gain	1.0000
12:132701245:TGCAG:T	acceptor_loss	1.0000
12:132701246:GCA:G	acceptor_loss	1.0000
12:132701247:CA:C	acceptor_loss	1.0000
12:132701247:CAG:C	acceptor_loss	1.0000
12:132701248:A:AC	acceptor_loss	1.0000
12:132701248:A:AG	acceptor_gain	1.0000
12:132701248:AG:A	acceptor_gain	1.0000
12:132701248:AGG:A	acceptor_gain	1.0000
12:132701248:AGGG:A	acceptor_gain	1.0000
12:132701249:G:GT	acceptor_gain	1.0000
12:132701249:GG:G	acceptor_gain	1.0000
12:132701249:GGG:G	acceptor_gain	1.0000
12:132701249:GGGG:G	acceptor_gain	1.0000
12:132701366:GAAG:G	donor_gain	1.0000
12:132701368:AGG:A	donor_loss	1.0000
12:132701369:GGTG:G	donor_loss	1.0000
12:132701370:G:GA	donor_loss	1.0000
12:132701370:GTGAG:G	donor_loss	1.0000

AlphaMissense

1258 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
12:132701348:C:A	N166K	0.986
12:132701348:C:G	N166K	0.986
12:132690265:G:A	G42D	0.985
12:132690376:G:A	G79E	0.985
12:132701359:T:A	V170D	0.985
12:132690264:G:C	G42R	0.979
12:132687791:A:C	S41R	0.978
12:132690263:T:A	S41R	0.978
12:132690263:T:G	S41R	0.978
12:132695897:G:T	G84W	0.978
12:132701344:T:A	I165N	0.978
12:132695906:A:C	S87R	0.977
12:132695908:T:A	S87R	0.977
12:132695908:T:G	S87R	0.977
12:132701315:C:A	N155K	0.977
12:132701315:C:G	N155K	0.977
12:132690375:G:T	G79W	0.976
12:132701316:T:A	W156R	0.976
12:132701316:T:C	W156R	0.976
12:132701327:G:C	W159C	0.976
12:132701327:G:T	W159C	0.976
12:132695898:G:A	G84E	0.975
12:132696020:T:C	F125L	0.974
12:132696022:C:A	F125L	0.974
12:132696022:C:G	F125L	0.974
12:132687782:G:C	A38P	0.972
12:132701325:T:A	W159R	0.972
12:132701325:T:C	W159R	0.972
12:132690367:C:A	A76D	0.970
12:132704639:C:A	N180K	0.969

dbSNP variants (sampled 300 via entrez): RS1000230189 (12:132705482 G>A), RS1000334479 (12:132699879 G>A,T), RS1000541182 (12:132691866 A>G), RS1000593110 (12:132685961 C>T), RS10007 (12:132704876 G>A), RS1000795616 (12:132705447 C>T), RS1000958627 (12:132702206 A>G), RS1001129293 (12:132699687 G>A), RS1001136456 (12:132696339 C>T), RS1001286705 (12:132704955 A>T), RS1001361950 (12:132691207 A>G), RS1001410417 (12:132699815 A>G), RS1001430551 (12:132685651 A>G), RS1001430822 (12:132687642 G>A,C,T), RS1001476439 (12:132687494 A>G)

Disease associations

OMIM: gene MIM:617399 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST90002387_131	Immature fraction of reticulocytes	5.000000e-12
GCST90002390_181	Mean corpuscular hemoglobin	7.000000e-13
GCST90002396_544	Mean reticulocyte volume	2.000000e-10
GCST90002397_53	Mean spheric corpuscular volume	3.000000e-11

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0004527	mean corpuscular hemoglobin
EFO:0010701	mean reticulocyte volume

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	affects expression, decreases expression	4
sodium arsenite	increases expression, decreases expression, affects cotreatment, increases abundance	3
Cyclosporine	decreases expression	3
Benzo(a)pyrene	decreases expression	2
Nickel	decreases expression	2
Ozone	affects expression, increases abundance, increases expression	2
sotorasib	affects cotreatment, increases expression	1
methylmercuric chloride	decreases expression	1
pirinixic acid	increases activity, affects binding, decreases expression	1
bisphenol A	affects expression	1
beta-lapachone	decreases expression	1
arsenite	affects binding, increases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
cobaltous chloride	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
periodate-oxidized adenosine	affects expression	1
perfluoro-n-nonanoic acid	decreases expression	1
K 7174	decreases expression	1
erucylphospho-N,N,N-trimethylpropylammonium	decreases expression	1
trametinib	affects cotreatment, increases expression	1
(+)-JQ1 compound	decreases expression	1
MT19c compound	decreases expression	1
NVP-BKM120	affects cotreatment, increases expression	1
Temozolomide	increases expression	1
Arsenic Trioxide	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	increases abundance, affects expression	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Cisplatin	increases expression	1
Hydrogen Peroxide	affects expression	1

Clinical trials (associated diseases)

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