PEX11A

Summary

PEX11A (peroxisomal biogenesis factor 11 alpha, HGNC:8852) is a protein-coding gene on chromosome 15q26.1, encoding Peroxisomal membrane protein 11A (O75192). May be involved in peroxisomal proliferation and may regulate peroxisomes division.

This gene is a member of the PEX11 family, which is composed of membrane elongation factors involved in regulation of peroxisome maintenance and proliferation. This gene product interacts with peroxisomal membrane protein 19 and may respond to outside stimuli to increase peroxisome abundance. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 8800 — RefSeq curated summary.

At a glance

• Gene–disease (curated): peroxisome biogenesis disorder (No Known Disease Relationship, ClinGen)
• GWAS associations: 1
• Clinical variants (ClinVar): 52 total
• MANE Select transcript: NM_003847

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8852
Approved symbol	PEX11A
Name	peroxisomal biogenesis factor 11 alpha
Location	15q26.1
Locus type	gene with protein product
Status	Approved
Aliases	PEX11alpha, PEX11α, PMP28, MGC119947, MGC138534
Ensembl gene	ENSG00000166821
Ensembl biotype	protein_coding
OMIM	603866
Entrez	8800

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 4 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000300056, ENST00000557982, ENST00000559170, ENST00000561224, ENST00000561257

RefSeq mRNA: 3 — MANE Select: NM_003847 NM_001271572, NM_001271573, NM_003847

CCDS: CCDS10354, CCDS61751

Canonical transcript exons

ENST00000300056 — 3 exons

Exon	Start	End
ENSE00001106937	89686431	89686546
ENSE00001270947	89681535	89683948
ENSE00003605988	89690577	89690754

Expression profiles

Bgee: expression breadth ubiquitous, 276 present calls, max score 88.64.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 4.5243 / max 37.3755, expressed in 1436 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
151476	4.2917	1428
151475	0.1686	103
151477	0.0640	22

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
jejunal mucosa	UBERON:0000399	88.64	gold quality
germinal epithelium of ovary	UBERON:0001304	88.02	gold quality
mucosa of transverse colon	UBERON:0004991	87.35	gold quality
parotid gland	UBERON:0001831	87.32	gold quality
colonic mucosa	UBERON:0000317	87.26	gold quality
adipose tissue	UBERON:0001013	86.78	gold quality
thoracic mammary gland	UBERON:0005200	86.53	gold quality
mammary gland	UBERON:0001911	86.52	gold quality
right lobe of liver	UBERON:0001114	86.41	gold quality
mucosa of sigmoid colon	UBERON:0004993	86.36	gold quality
palpebral conjunctiva	UBERON:0001812	86.13	gold quality
subcutaneous adipose tissue	UBERON:0002190	86.11	gold quality
liver	UBERON:0002107	86.09	gold quality
parietal pleura	UBERON:0002400	86.00	gold quality
secondary oocyte	CL:0000655	85.90	gold quality
connective tissue	UBERON:0002384	85.83	gold quality
adipose tissue of abdominal region	UBERON:0007808	85.22	gold quality
omental fat pad	UBERON:0010414	84.94	gold quality
peritoneum	UBERON:0002358	84.92	gold quality
duodenum	UBERON:0002114	84.72	gold quality
pigmented layer of retina	UBERON:0001782	84.70	gold quality
gastrocnemius	UBERON:0001388	84.67	gold quality
esophagus squamous epithelium	UBERON:0006920	84.15	gold quality
muscle of leg	UBERON:0001383	84.13	gold quality
choroid plexus epithelium	UBERON:0003911	83.90	gold quality
tendon of biceps brachii	UBERON:0008188	83.85	gold quality
mucosa of stomach	UBERON:0001199	83.62	gold quality
islet of Langerhans	UBERON:0000006	83.56	gold quality
pleura	UBERON:0000977	83.36	gold quality
epithelium of mammary gland	UBERON:0003244	83.28	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.24

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): PPARA, PPARG

miRNA regulators (miRDB)

74 targeting PEX11A, 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-LET-7A-3P	100.00	74.03	3932
HSA-MIR-513A-5P	100.00	69.77	2465
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-4775	99.98	75.00	6394
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-23A-3P	99.95	74.24	3163
HSA-MIR-23B-3P	99.95	74.24	3163
HSA-MIR-23C	99.95	73.92	3192
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-4306	99.72	70.50	3630
HSA-MIR-7154-5P	99.69	70.52	1900
HSA-MIR-580-3P	99.67	69.23	1841
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-6757-3P	99.63	66.88	1089
HSA-MIR-4328	99.57	71.06	4094
HSA-MIR-3942-3P	99.57	69.03	2854
HSA-MIR-12122	99.56	69.33	1672
HSA-MIR-12123	99.52	71.79	2990
HSA-MIR-4437	99.52	65.29	1266
HSA-MIR-513C-5P	99.50	68.42	1730
HSA-MIR-514B-5P	99.50	68.19	1766
HSA-MIR-5584-5P	99.49	68.22	2814

Literature-anchored findings (GeneRIF, showing 3)

• Mice lacking PEX11-alpha have normal peroxisome abundance. (PMID:12417726)
• Cooperation with other transcription factors may be differentially involved in selective transactivation of the PEX11alpha gene by different peroxisome proliferator-activated receptor subtypes. (PMID:16567422)
• coordinates peroxisome membrane proliferation and maintenance (PMID:20826455)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	pex11a	ENSDARG00000060707
mus_musculus	Pex11a	ENSMUSG00000030545
rattus_norvegicus	Pex11a	ENSRNOG00000015003
drosophila_melanogaster	Pex11ab	FBGN0034058

Paralogs (1): PEX11B (ENSG00000131779)

Protein

Protein identifiers

Peroxisomal membrane protein 11A — O75192 (reviewed: O75192)

Alternative names: 28 kDa peroxisomal integral membrane protein, Peroxin-11A, Peroxisomal biogenesis factor 11A, Protein PEX11 homolog alpha

All UniProt accessions (4): O75192, B2R8C6, H0YMC7, H0YN61

UniProt curated annotations — full annotation on UniProt →

Function. May be involved in peroxisomal proliferation and may regulate peroxisomes division. May mediate binding of coatomer proteins to the peroxisomal membrane. Promotes membrane protrusion and elongation on the peroxisomal surface.

Subunit / interactions. Homodimer. Heterodimer with PEX11G. Probably interacts with COPB2 and COPA. Interacts with PEX19. Interacts with FIS1.

Subcellular location. Peroxisome membrane.

Post-translational modifications. Does not seem to be N-glycosylated.

Similarity. Belongs to the peroxin-11 family.

Isoforms (2)

UniProt ID	Names	Canonical?
O75192-1	1	yes
O75192-2	2

RefSeq proteins (3): NP_001258501, NP_001258502, NP_003838* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008733	PEX11	Family

Pfam: PF05648

UniProt features (10 total): topological domain 3, transmembrane region 2, mutagenesis site 2, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O75192-F1	88.09	0.62

Functional residue map

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

Mutagenesis-validated functional residues (2):

Position	Phenotype
9	no effect on peroxisomal location.
243–245	no effect on peroxisomal location.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

ID	Pathway
R-HSA-1989781	PPARA activates gene expression
R-HSA-9841922	MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis

MSigDB gene sets: 154 (showing top): CLAUS_PGR_POSITIVE_MENINGIOMA_UP, GOBP_MEMBRANE_BIOGENESIS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_SIZE, GOBP_ORGANELLE_FISSION, ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN, GOBP_BROWN_FAT_CELL_DIFFERENTIATION, GOBP_FAT_CELL_DIFFERENTIATION, LEE_LIVER_CANCER_DENA_DN, GOCC_MICROBODY_MEMBRANE, RUAN_RESPONSE_TO_TNF_DN, BURTON_ADIPOGENESIS_5, LIU_SOX4_TARGETS_DN, GOCC_MICROBODY

GO Biological Process (6): peroxisome organization (GO:0007031), signal transduction (GO:0007165), peroxisome membrane biogenesis (GO:0016557), peroxisome fission (GO:0016559), regulation of peroxisome size (GO:0044375), brown fat cell differentiation (GO:0050873)

GO Molecular Function (2): protein homodimerization activity (GO:0042803), protein binding (GO:0005515)

GO Cellular Component (4): peroxisome (GO:0005777), peroxisomal membrane (GO:0005778), protein-containing complex (GO:0032991), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Regulation of lipid metabolism by PPARalpha	1
Epigenetic regulation of adipogenesis genes by MLL3 and MLL4 complexes	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
peroxisome organization	2
organelle organization	1
cell communication	1
cellular process	1
signaling	1
regulation of cellular process	1
cellular response to stimulus	1
membrane biogenesis	1
organelle fission	1
regulation of cellular component size	1
fat cell differentiation	1
identical protein binding	1
protein dimerization activity	1
binding	1
microbody	1
peroxisome	1
microbody membrane	1
cellular_component	1
cellular anatomical structure	1

Protein interactions and networks

STRING

1022 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PEX11A	PEX11G	Q96HA9	969
PEX11A	FIS1	Q9Y3D6	961
PEX11A	DNM1L	O00429	909
PEX11A	PEX12	O00623	860
PEX11A	PEX19	P40855	857
PEX11A	PEX13	Q92968	847
PEX11A	PEX3	P56589	844
PEX11A	PEX16	Q9Y5Y5	840
PEX11A	PEX10	O60683	838
PEX11A	PEX6	Q13608	837
PEX11A	PEX5	P50542	831
PEX11A	PEX7	O00628	810
PEX11A	PEX2	P28328	809
PEX11A	PPARA	Q07869	795
PEX11A	DNM1	Q05193	778

IntAct

7 interactions, top by confidence:

A	B	Type	Score
SLC30A2	ESYT2	psi-mi:“MI:0914”(association)	0.530
PEX11A	SUFU	psi-mi:“MI:0915”(physical association)	0.400
PEX11A	PEX11A	psi-mi:“MI:0915”(physical association)	0.400
PEX11G	PEX11A	psi-mi:“MI:0915”(physical association)	0.400
PEX11A	FIS1	psi-mi:“MI:0915”(physical association)	0.400
PEX11A	HERC1	psi-mi:“MI:0914”(association)	0.350

BioGRID (15): SUFU (Affinity Capture-MS), PEX11A (Proximity Label-MS), NEDD8-MDP1 (Affinity Capture-MS), VCPIP1 (Affinity Capture-MS), HERC1 (Affinity Capture-MS), AMER1 (Cross-Linking-MS (XL-MS)), CBX3 (Cross-Linking-MS (XL-MS)), PEX11A (Cross-Linking-MS (XL-MS)), PEX11A (Affinity Capture-MS), DNM1L (Phenotypic Enhancement), FIS1 (Phenotypic Suppression), PEX11A (Affinity Capture-Western), PEX11A (Affinity Capture-Western), FIS1 (Affinity Capture-Western), PEX11A (Protein-peptide)

ESM2 similar proteins: A2XFC1, A2XFQ8, B0JYZ2, B4FBQ7, B6SR79, B8AK78, B9FGV7, C5WNF5, C5YDQ9, F2EL82, O70597, O75192, Q01IH3, Q01IJ3, Q0DSV9, Q0VCP2, Q10CI8, Q10MN2, Q10MN3, Q10MR5, Q10PZ4, Q2QTL0, Q4QRH7, Q5N9A1, Q5VQG8, Q5ZEG0, Q69P80, Q6ATB4, Q6EUK7, Q6INN0, Q6P6M5, Q6YSY5, Q6Z517, Q7X745, Q7XR51, Q7XTQ5, Q7XU74, Q7ZVP8, Q8LFP1, Q8RWG3

Diamond homologs: O70597, O75192, O96011, Q0VCP2, Q148K5, Q5RFI0, Q9Z210, Q9Z211

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	45
Likely benign	3
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

480 predictions. Top by Δscore:

Variant	Effect	Δscore
15:89686423:GTAC:G	donor_loss	1.0000
15:89686424:TACT:T	donor_loss	1.0000
15:89686425:ACTTA:A	donor_loss	1.0000
15:89686426:CT:C	donor_loss	1.0000
15:89686427:TTA:T	donor_loss	1.0000
15:89686428:TACAT:T	donor_loss	1.0000
15:89686429:A:AC	donor_gain	1.0000
15:89686429:ACATT:A	donor_loss	1.0000
15:89686430:C:CC	donor_gain	1.0000
15:89686430:C:T	donor_loss	1.0000
15:89690572:CTCA:C	donor_loss	1.0000
15:89690575:A:AC	donor_gain	1.0000
15:89690576:C:CC	donor_gain	1.0000
15:89679263:C:A	donor_gain	0.9900
15:89679320:A:AC	donor_gain	0.9900
15:89679321:C:CC	donor_gain	0.9900
15:89686422:GGTAC:G	donor_loss	0.9900
15:89686430:CA:C	donor_gain	0.9900
15:89686430:CATTT:C	donor_gain	0.9900
15:89686544:GCTC:G	acceptor_loss	0.9900
15:89686545:CT:C	acceptor_gain	0.9900
15:89686546:TC:T	acceptor_loss	0.9900
15:89686547:C:A	acceptor_loss	0.9900
15:89686547:C:CC	acceptor_gain	0.9900
15:89686548:T:G	acceptor_loss	0.9900
15:89679245:CCTTA:C	donor_loss	0.9800
15:89679246:CTTA:C	donor_loss	0.9800
15:89679247:TTA:T	donor_loss	0.9800
15:89679248:TAC:T	donor_loss	0.9800
15:89679249:A:AT	donor_loss	0.9800

AlphaMissense

1599 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:89686436:C:G	R56P	0.981
15:89686437:G:T	R56S	0.981
15:89683942:C:G	R60T	0.979
15:89690577:C:G	R19T	0.977
15:89683941:T:A	R60S	0.976
15:89683941:T:G	R60S	0.976
15:89683766:A:G	W119R	0.974
15:89683766:A:T	W119R	0.974
15:89683811:A:G	W104R	0.974
15:89683811:A:T	W104R	0.974
15:89686546:T:A	R19S	0.974
15:89686546:T:G	R19S	0.974
15:89686530:A:G	C25R	0.973
15:89683521:C:A	K200N	0.970
15:89683521:C:G	K200N	0.970
15:89690577:C:A	R19I	0.970
15:89690592:C:G	R14P	0.964
15:89683453:C:T	G223E	0.963
15:89683822:T:G	D100A	0.962
15:89683822:T:A	D100V	0.961
15:89683936:C:T	G62D	0.961
15:89683432:G:A	S230F	0.960
15:89683514:A:G	C203R	0.960
15:89686431:A:G	W58R	0.960
15:89686431:A:T	W58R	0.960
15:89690586:C:G	R16P	0.959
15:89690596:C:G	G13R	0.959
15:89686439:C:T	G55D	0.958
15:89683444:C:T	G226D	0.955
15:89686545:C:G	A20P	0.952

dbSNP variants (sampled 300 via entrez): RS1000056804 (15:89684353 G>A), RS1000409799 (15:89689767 C>A), RS1000417638 (15:89683264 C>T), RS1000752627 (15:89681771 C>A,T), RS1000864526 (15:89691680 A>G), RS1001138726 (15:89688486 G>A), RS1001475121 (15:89686121 C>T), RS1002211605 (15:89692738 C>CTGGG), RS1002308633 (15:89687169 C>G,T), RS1002411231 (15:89686975 T>G), RS1002530347 (15:89687247 C>A), RS1002645503 (15:89685545 C>T), RS1003038527 (15:89692064 G>C), RS1003157196 (15:89687670 G>A), RS1004317960 (15:89690550 G>C)

Disease associations

OMIM: gene MIM:603866 | disease phenotypes:

GenCC curated gene-disease

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

Disease	Classification	Inheritance
peroxisome biogenesis disorder	No Known Disease Relationship	AR

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST008839_429	Height	3.000000e-10

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
bisphenol A	increases expression, decreases expression, increases methylation, affects cotreatment	2
perfluorooctanoic acid	increases expression	2
Nickel	decreases expression	2
Valproic Acid	decreases expression, increases expression	2
Cyclosporine	decreases expression	2
Aflatoxin B1	decreases expression, increases methylation	2
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
trichostatin A	increases expression	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
sodium arsenite	decreases expression, increases expression	1
ferrous chloride	decreases expression	1
cupric chloride	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	decreases reaction, decreases expression	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	affects expression	1
paricalcitol	affects cotreatment, affects expression	1
perfluorohexanesulfonic acid	increases expression	1
abrine	decreases expression	1
Rosiglitazone	increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Temozolomide	decreases expression	1
Sunitinib	decreases expression	1
Leflunomide	decreases expression	1
Acetaminophen	decreases expression	1
Atrazine	decreases expression	1
Dexamethasone	affects cotreatment, increases expression	1
Estradiol	increases expression, decreases reaction	1
Indomethacin	affects cotreatment, increases expression	1

Clinical trials (associated diseases)

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