PEX39

Summary

PEX39 (peroxisomal biogenesis factor 39, HGNC:34431) is a protein-coding gene on chromosome 6p21.1, encoding Peroxisomal biogenesis factor 39 (Q5I0X4). May be a peroxin involved in the PTS2-mediated protein import pathway.

Predicted to be located in peroxisome.

Source: NCBI Gene 441150 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• MANE Select transcript: NM_001008739

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34431
Approved symbol	PEX39
Name	peroxisomal biogenesis factor 39
Location	6p21.1
Locus type	gene with protein product
Status	Approved
Aliases	LOC441150
Ensembl gene	ENSG00000221821
Ensembl biotype	protein_coding
Entrez	441150

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000408925

RefSeq mRNA: 1 — MANE Select: NM_001008739 NM_001008739

CCDS: CCDS43463

Canonical transcript exons

ENST00000408925 — 1 exons

Exon	Start	End
ENSE00001574993	42890265	42890821

Expression profiles

Bgee: expression breadth ubiquitous, 209 present calls, max score 90.21.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.5111 / max 105.4792, expressed in 1748 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
73640	15.5111	1748

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right adrenal gland	UBERON:0001233	90.21	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	90.18	gold quality
left adrenal gland cortex	UBERON:0035825	89.90	gold quality
right adrenal gland cortex	UBERON:0035827	89.80	gold quality
left adrenal gland	UBERON:0001234	89.71	gold quality
adenohypophysis	UBERON:0002196	88.62	gold quality
adrenal cortex	UBERON:0001235	88.49	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	88.04	gold quality
mucosa of stomach	UBERON:0001199	88.04	gold quality
pituitary gland	UBERON:0000007	86.79	gold quality
skin of leg	UBERON:0001511	86.65	gold quality
hypothalamus	UBERON:0001898	86.33	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	86.24	gold quality
right lung	UBERON:0002167	86.18	gold quality
adrenal gland	UBERON:0002369	86.10	gold quality
lower esophagus muscularis layer	UBERON:0035833	85.89	gold quality
lower esophagus	UBERON:0013473	85.84	gold quality
apex of heart	UBERON:0002098	85.75	gold quality
monocyte	CL:0000576	85.57	gold quality
tibial artery	UBERON:0007610	85.55	gold quality
popliteal artery	UBERON:0002250	85.53	gold quality
leukocyte	CL:0000738	85.40	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	85.40	gold quality
skin of abdomen	UBERON:0001416	85.39	gold quality
putamen	UBERON:0001874	85.09	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.03	silver quality
muscle layer of sigmoid colon	UBERON:0035805	85.00	gold quality
nucleus accumbens	UBERON:0001882	84.81	gold quality
granulocyte	CL:0000094	84.76	gold quality
mucosa of transverse colon	UBERON:0004991	84.60	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)

7 targeting PEX39, 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-4719	99.73	72.10	3329
HSA-MIR-4422	99.72	72.07	2908
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-876-3P	98.76	68.23	945
HSA-MIR-4722-5P	98.46	66.34	1611
HSA-MIR-3169	96.40	67.58	698
HSA-MIR-4740-5P	96.25	67.96	726

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pex39	ENSMUSG00000062619
rattus_norvegicus	C9h6orf226	ENSRNOG00000079593

Protein

Protein identifiers

Peroxisomal biogenesis factor 39 — Q5I0X4 (reviewed: Q5I0X4)

All UniProt accessions (1): Q5I0X4

UniProt curated annotations — full annotation on UniProt →

Function. May be a peroxin involved in the PTS2-mediated protein import pathway.

Subcellular location. Peroxisome.

RefSeq proteins (1): NP_001008739* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR039995	PEX39	Family
IPR040554	KPWE_PEX14_dom	Domain

Pfam: PF17733

UniProt features (1 total): chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5I0X4-F1	71.85	0.18

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 49 (showing top): ACEVEDO_LIVER_CANCER_UP, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, GOCC_MICROBODY, LU_EZH2_TARGETS_UP, WIERENGA_STAT5A_TARGETS_DN, VANOEVELEN_MYOGENESIS_SIN3A_TARGETS, BOUDOUKHA_BOUND_BY_IGF2BP2, EIF4E_UP, ATF6_TARGET_GENES, CHAF1B_TARGET_GENES, EMX1_TARGET_GENES, HES4_TARGET_GENES, NFE2L1_TARGET_GENES, OVOL3_TARGET_GENES, SKIL_TARGET_GENES

GO Biological Process (0):

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

GO Cellular Component (1): peroxisome (GO:0005777)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
microbody	1

Protein interactions and networks

STRING

156 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PEX39	A0A0J9YXS1	A0A0J9YXS1	662
PEX39	C1orf122	Q6ZSJ8	507
PEX39	TIGD5	Q53EQ6	507
PEX39	B8ZZ87	B8ZZ87	480
PEX39	EFCAB5	A4FU69	447
PEX39	SLX9	Q9NSI2	444
PEX39	ZNF358	Q9NW07	435
PEX39	SLC33A2	Q96ES6	419
PEX39	NECAP2	Q9NVZ3	419
PEX39	SCAND1	P57086	394
PEX39	RRP1B	Q14684	378
PEX39	DNPH1	O43598	373
PEX39	ALDH16A1	Q8IZ83	373
PEX39	ALKBH7	Q9BT30	370
PEX39	LY6G6C	O95867	370

IntAct

29 interactions, top by confidence:

A	B	Type	Score
APPBP2	PEX39	psi-mi:“MI:0915”(physical association)	0.720
PEX39	APPBP2	psi-mi:“MI:0915”(physical association)	0.720
PEX39	CCNDBP1	psi-mi:“MI:0915”(physical association)	0.670
PEX39	HNRNPK	psi-mi:“MI:0915”(physical association)	0.670
CCNDBP1	PEX39	psi-mi:“MI:0915”(physical association)	0.670
HNRNPK	PEX39	psi-mi:“MI:0915”(physical association)	0.670
KRT40	PEX39	psi-mi:“MI:0915”(physical association)	0.560
PEX39	TEX11	psi-mi:“MI:0915”(physical association)	0.560
PEX39	KRT40	psi-mi:“MI:0915”(physical association)	0.560
TEX11	PEX39	psi-mi:“MI:0915”(physical association)	0.560
PEX39	PEX7	psi-mi:“MI:0914”(association)	0.530
ACAA1	PEX7	psi-mi:“MI:0914”(association)	0.530
PHYH	PEX7	psi-mi:“MI:0914”(association)	0.350
PEX7	PFDN6	psi-mi:“MI:0914”(association)	0.350
PEX39	APPBP2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (18): C6orf226 (Two-hybrid), C6orf226 (Two-hybrid), C6orf226 (Two-hybrid), C6orf226 (Two-hybrid), C6orf226 (Two-hybrid), C6orf226 (Affinity Capture-MS), C6orf226 (Affinity Capture-MS), ACAA1 (Affinity Capture-MS), PEX7 (Affinity Capture-MS), PHYH (Affinity Capture-MS), C6orf226 (Two-hybrid), C6orf226 (Two-hybrid), ACAA1 (Affinity Capture-MS), PEX7 (Affinity Capture-MS), PHYH (Affinity Capture-MS)

ESM2 similar proteins: A0A1D5AG16, A4Y0M0, A8IYS6, A8QA64, C6FX52, G2WWH6, J9VQE5, O13904, O18811, O68586, O83706, P0C8B4, P0C8B5, P0C8P9, P31962, P31963, P34069, P34166, P56650, P78742, P78743, P97516, P9WES8, P9WL02, P9WL03, Q02594, Q12373, Q2PE14, Q4PDA7, Q4RTJ5, Q4W9G3, Q4WIN1, Q5I0X4, Q62857, Q67593, Q69T21, Q6CHP5, Q753S8, Q75DE8, Q75E62

Diamond homologs: Q5I0X4, Q9D727

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

136 predictions. Top by Δscore:

Variant	Effect	Δscore
6:42890691:T:TA	donor_gain	0.9200
6:42890620:T:TA	donor_gain	0.8900
6:42890559:AT:A	donor_gain	0.7900
6:42890588:A:AC	donor_gain	0.7900
6:42890604:T:TA	donor_gain	0.7900
6:42890806:G:T	donor_gain	0.7800
6:42890784:T:A	donor_gain	0.7700
6:42890560:T:TA	donor_gain	0.7600
6:42890636:CG:C	donor_gain	0.7400
6:42890588:AGC:A	donor_gain	0.7300
6:42890649:C:CA	donor_gain	0.7200
6:42890785:C:CA	donor_gain	0.7200
6:42890739:G:C	donor_gain	0.7000
6:42890648:G:A	donor_gain	0.6700
6:42890697:C:CA	donor_gain	0.6700
6:42890601:G:GA	donor_gain	0.6500
6:42890529:A:C	donor_gain	0.6400
6:42890318:A:C	donor_gain	0.6200
6:42890803:C:A	donor_gain	0.6200
6:42890449:C:CA	donor_gain	0.6100
6:42890802:T:TA	donor_gain	0.6000
6:42890526:TCA:T	donor_gain	0.5900
6:42890555:T:A	donor_gain	0.5900
6:42890485:AGGGG:A	donor_gain	0.5600
6:42890418:A:C	donor_gain	0.5500
6:42890621:C:CA	donor_gain	0.5500
6:42890493:A:AC	donor_gain	0.5300
6:42890696:G:A	donor_gain	0.5300
6:42890523:G:GA	donor_gain	0.5200
6:42890614:TGG:T	donor_gain	0.5100

AlphaMissense

618 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:42890606:C:A	W61C	0.991
6:42890606:C:G	W61C	0.991
6:42890612:C:A	K59N	0.987
6:42890612:C:G	K59N	0.987
6:42890608:A:G	W61R	0.985
6:42890608:A:T	W61R	0.985
6:42890718:A:G	L24P	0.971
6:42890614:T:C	K59E	0.967
6:42890706:A:T	V28D	0.963
6:42890613:T:G	K59T	0.960
6:42890607:C:A	W61L	0.956
6:42890604:T:A	E62V	0.949
6:42890603:C:A	E62D	0.942
6:42890603:C:G	E62D	0.942
6:42890604:T:C	E62G	0.937
6:42890607:C:G	W61S	0.933
6:42890697:C:A	G31V	0.916
6:42890613:T:A	K59M	0.912
6:42890614:T:G	K59Q	0.909
6:42890715:A:G	L25P	0.903
6:42890709:A:G	L27P	0.900
6:42890605:C:T	E62K	0.894
6:42890604:T:G	E62A	0.890
6:42890608:A:C	W61G	0.889
6:42890718:A:T	L24H	0.884
6:42890730:G:A	T20I	0.872
6:42890643:G:T	P49H	0.867
6:42890664:A:T	I42N	0.861
6:42890698:C:G	G31R	0.852
6:42890698:C:A	G31C	0.849

dbSNP variants (sampled 300 via entrez): RS1000382508 (6:42892536 G>A,C), RS1002628128 (6:42890939 T>A,C), RS1003223887 (6:42889812 C>T), RS1004055453 (6:42890707 C>A,G,T), RS1004986807 (6:42891007 G>A,T), RS1005991509 (6:42892272 A>G), RS1009550364 (6:42890319 C>T), RS1010611498 (6:42891442 G>T), RS1011089297 (6:42889915 G>A), RS1012532578 (6:42891855 C>T), RS1013554868 (6:42891335 T>C), RS1013787128 (6:42891109 C>G,T), RS1014824197 (6:42892305 T>C), RS1015230206 (6:42890780 A>T), RS1016520994 (6:42891664 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST90002395_473	Mean platelet volume	2.000000e-23

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression	3
Benzo(a)pyrene	decreases methylation, increases expression	2
GSK-J4	decreases expression	1
dicrotophos	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	decreases expression, affects cotreatment	1
dorsomorphin	decreases expression, affects cotreatment	1
jinfukang	increases expression	1
(+)-JQ1 compound	increases expression	1
Diethylhexyl Phthalate	decreases expression	1
Quercetin	increases expression	1
Smoke	decreases expression	1
Thiram	increases expression	1
Aflatoxin B1	increases expression	1
Cadmium Chloride	increases expression	1
Okadaic Acid	decreases expression	1
Lactic Acid	decreases expression	1
Acrylamide	decreases expression	1

Clinical trials (associated diseases)

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