PXT1

Summary

PXT1 (peroxisomal testis enriched protein 1, HGNC:18312) is a protein-coding gene on chromosome 6p21.31, encoding Peroxisomal testis-specific protein 1 (Q8NFP0).

Predicted to be involved in spermatogenesis. Predicted to act upstream of or within positive regulation of apoptotic process. Predicted to be located in nucleus and peroxisome.

Source: NCBI Gene 222659 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 23 total
• MANE Select transcript: NM_152990

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18312
Approved symbol	PXT1
Name	peroxisomal testis enriched protein 1
Location	6p21.31
Locus type	gene with protein product
Status	Approved
Aliases	STEPP
Ensembl gene	ENSG00000179165
Ensembl biotype	protein_coding
Entrez	222659

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000454782

RefSeq mRNA: 1 — MANE Select: NM_152990 NM_152990

CCDS: CCDS4820

Canonical transcript exons

ENST00000454782 — 5 exons

Exon	Start	End
ENSE00001236015	36390551	36391874
ENSE00001638918	36438767	36438886
ENSE00001675576	36442535	36442854
ENSE00001763444	36425914	36426091
ENSE00001792178	36400454	36400584

Expression profiles

Bgee: expression breadth broad, 88 present calls, max score 75.77.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2947 / max 62.7100, expressed in 110 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
73347	0.2947	110

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.77	gold quality
right testis	UBERON:0004534	59.37	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	59.34	gold quality
left testis	UBERON:0004533	58.88	gold quality
testis	UBERON:0000473	57.58	gold quality
cortical plate	UBERON:0005343	53.70	gold quality
gastrocnemius	UBERON:0001388	50.74	gold quality
skin of hip	UBERON:0001554	49.44	silver quality
muscle of leg	UBERON:0001383	49.42	gold quality
blood	UBERON:0000178	48.22	gold quality
bone marrow cell	CL:0002092	47.44	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	46.63	gold quality
upper leg skin	UBERON:0004262	45.56	silver quality
tibial nerve	UBERON:0001323	45.12	gold quality
cerebellar cortex	UBERON:0002129	44.34	gold quality
prefrontal cortex	UBERON:0000451	44.33	gold quality
ventricular zone	UBERON:0003053	44.12	silver quality
cerebellar hemisphere	UBERON:0002245	44.05	gold quality
cerebellum	UBERON:0002037	43.85	gold quality
nasal cavity mucosa	UBERON:0001826	43.53	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
ganglionic eminence	UBERON:0004023	43.19	gold quality
bone marrow	UBERON:0002371	43.18	silver quality
heart left ventricle	UBERON:0002084	42.77	gold quality
cardiac ventricle	UBERON:0002082	42.67	gold quality
mucosa of stomach	UBERON:0001199	42.59	silver quality
secondary oocyte	CL:0000655	42.57	gold quality
vastus lateralis	UBERON:0001379	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.91

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

74 targeting PXT1, 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-4533	100.00	69.48	2758
HSA-MIR-4510	100.00	66.60	2050
HSA-MIR-6127	100.00	66.76	2188
HSA-MIR-6129	100.00	66.46	2080
HSA-MIR-6130	100.00	66.69	2012
HSA-MIR-6133	100.00	66.48	2064
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4747-5P	100.00	67.90	2681
HSA-MIR-5196-5P	100.00	67.98	2761
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-4500	99.99	72.72	2367
HSA-MIR-3185	99.99	68.12	1959
HSA-LET-7A-5P	99.98	72.29	1790
HSA-LET-7B-5P	99.98	72.31	1790
HSA-LET-7C-5P	99.98	72.29	1790
HSA-LET-7E-5P	99.98	72.29	1790
HSA-LET-7F-5P	99.98	72.56	1784
HSA-LET-7G-5P	99.98	72.37	1784
HSA-LET-7I-5P	99.98	72.37	1788
HSA-MIR-98-5P	99.98	72.33	1787
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-LET-7D-5P	99.96	71.76	1632
HSA-MIR-4458	99.96	71.64	1650
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-202-3P	99.84	71.41	1290
HSA-MIR-130B-5P	99.83	68.50	1888
HSA-MIR-3180-5P	99.82	69.12	2422
HSA-MIR-4495	99.82	72.08	3080

Literature-anchored findings (GeneRIF, showing 2)

• Pxt1 gene is so far the first gene coding for a putative peroxisomal protein which is expressed in later steps of spermatogenesis, namely in pachytene spermatocytes (PMID:18160785)
• Data show that CCDC33-dsRED fusion protein co-localized with a known peroxisomal protein, namely PXT1, and showed punctuate intracellular distribution. (PMID:20068295)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Pxt1	ENSMUSG00000045378
rattus_norvegicus	Pxt1	ENSRNOG00000000516

Protein

Protein identifiers

Peroxisomal testis-specific protein 1 — Q8NFP0 (reviewed: Q8NFP0)

Alternative names: Small testis-specific peroxisomal protein

All UniProt accessions (1): Q8NFP0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Peroxisome.

RefSeq proteins (1): NP_694535* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029186	PXT1	Family

Pfam: PF15214

UniProt features (4 total): chain 1, short sequence motif 1, sequence conflict 1, helix 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7WJH	X-RAY DIFFRACTION	1.7
8GSV	X-RAY DIFFRACTION	2.2

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NFP0-F1	67.79	0.16

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 49 (showing top): GOCC_MICROBODY, GSE13522_WT_VS_IFNG_KO_SKING_T_CRUZI_Y_STRAIN_INF_UP, E2F5_TARGET_GENES, SKIL_TARGET_GENES, TOP2B_TARGET_GENES, ZNF175_TARGET_GENES, ZNF7_TARGET_GENES, ZNF766_TARGET_GENES, MIR4306, MIR4500, MIR7159_5P, LET_7B_5P, LET_7A_5P_LET_7C_5P_LET_7E_5P, LET_7I_5P, LET_7F_5P

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

342 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PXT1	PEX13	Q92968	509
PXT1	LMOD2	Q6P5Q4	463
PXT1	KCTD20	Q7Z5Y7	445
PXT1	GNPAT	O15228	443
PXT1	RTN1	Q16799	440
PXT1	APOL6	Q9BWW8	421
PXT1	BNIP5	P0C671	419
PXT1	NKX1-1	Q15270	417
PXT1	RFX8	Q6ZV50	416
PXT1	INCA1	Q0VD86	404
PXT1	APOL2	Q9BQE5	400
PXT1	ZNF442	Q9H7R0	398
PXT1	TNP2	Q05952	397
PXT1	HLA-DQB1	P01917	383
PXT1	UBN2	Q6ZU65	377

IntAct

4 interactions, top by confidence:

A	B	Type	Score
MEOX2	PXT1	psi-mi:“MI:0915”(physical association)	0.560
PXT1	MEOX2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (1): PXT1 (Two-hybrid)

ESM2 similar proteins: A0A023PXL7, A0A023PXP4, A0A023PZG0, A0A182BSS4, B3SRR0, B3SRT4, B3SRV0, B3SRX4, O30049, O30086, P03939, P07116, P09504, P0C5B8, P0C5P9, P0CL34, P0CL35, P0CL36, P0CL37, P0CL38, P0CL39, P0CL40, P0CV18, P0CV26, P0CX94, P0CX95, P0CX96, P0CX97, P0CX98, P0CX99, P0CY00, P0CY01, P13893, P16814, P22754, P23691, P25215, P36074, P40097, P92542

Diamond homologs: Q8K459, Q8NFP0

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	20
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1155 predictions. Top by Δscore:

Variant	Effect	Δscore
6:36400448:CCTCA:C	donor_loss	0.9900
6:36400449:CTCA:C	donor_loss	0.9900
6:36400452:A:AG	donor_loss	0.9900
6:36400581:TGAT:T	acceptor_gain	0.9900
6:36400453:CCT:C	donor_gain	0.9800
6:36400583:ATCT:A	acceptor_loss	0.9800
6:36400584:TC:T	acceptor_loss	0.9800
6:36400585:C:CC	acceptor_gain	0.9800
6:36400585:C:CG	acceptor_loss	0.9800
6:36400587:G:C	acceptor_loss	0.9700
6:36400590:T:TC	acceptor_gain	0.9700
6:36423986:TC:T	donor_gain	0.9700
6:36425908:TCTTA:T	donor_loss	0.9700
6:36425909:CTTA:C	donor_loss	0.9700
6:36425910:TTA:T	donor_loss	0.9700
6:36425911:T:TG	donor_loss	0.9700
6:36425912:A:AG	donor_loss	0.9700
6:36425913:CCT:C	donor_loss	0.9700
6:36426089:TCCCT:T	acceptor_loss	0.9700
6:36426090:CC:C	acceptor_gain	0.9700
6:36426090:CCCTG:C	acceptor_loss	0.9700
6:36426091:CC:C	acceptor_gain	0.9700
6:36426091:CCTGT:C	acceptor_loss	0.9700
6:36426092:C:CG	acceptor_loss	0.9700
6:36426093:T:A	acceptor_loss	0.9700
6:36426094:G:C	acceptor_loss	0.9700
6:36442769:A:AC	donor_gain	0.9700
6:36442770:C:CC	donor_gain	0.9700
6:36391814:CTCTT:C	acceptor_gain	0.9600
6:36425907:ATCTT:A	donor_loss	0.9600

AlphaMissense

910 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:36400497:A:G	L86P	0.875
6:36400486:C:A	G90W	0.732
6:36400485:C:T	G90E	0.712
6:36400497:A:T	L86Q	0.684
6:36400507:C:G	A83P	0.683
6:36425963:C:A	M40I	0.676
6:36425963:C:G	M40I	0.676
6:36425963:C:T	M40I	0.676
6:36400497:A:C	L86R	0.671
6:36391836:A:C	F113L	0.668
6:36391836:A:T	F113L	0.668
6:36391838:A:G	F113L	0.668
6:36400493:T:A	R87S	0.655
6:36400493:T:G	R87S	0.655
6:36391821:A:C	F118L	0.642
6:36391821:A:T	F118L	0.642
6:36391823:A:G	F118L	0.642
6:36400485:C:A	G90V	0.635
6:36400486:C:G	G90R	0.621
6:36400486:C:T	G90R	0.621
6:36425978:A:C	F35L	0.621
6:36425978:A:T	F35L	0.621
6:36425980:A:G	F35L	0.621
6:36400509:A:G	L82S	0.599
6:36400506:G:T	A83D	0.578
6:36400482:T:A	D91V	0.574

dbSNP variants (sampled 300 via entrez): RS1000024494 (6:36402188 G>A), RS1000050759 (6:36421977 C>G), RS1000093132 (6:36403855 G>C), RS1000111346 (6:36408727 T>A,C), RS1000188805 (6:36408233 A>G), RS1000306010 (6:36400042 C>G,T), RS1000377021 (6:36399550 G>A), RS1000448544 (6:36407113 A>G), RS1000448637 (6:36421910 A>T), RS1000462992 (6:36401916 C>A), RS1000471703 (6:36421489 T>C), RS1000488585 (6:36407101 G>A), RS1000514611 (6:36442434 G>GT), RS1000526077 (6:36406775 T>C), RS1000535137 (6:36393707 C>G)

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

2 associations (top):

Study	Trait	p-value
GCST004599_227	Mean platelet volume	6.000000e-21
GCST005531_43	Multiple sclerosis	4.000000e-10

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation	1
Demecolcine	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Formaldehyde	increases expression	1
Methyl Methanesulfonate	increases expression	1
Vincristine	increases expression	1

Clinical trials (associated diseases)

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