PEX3 (peroxisomal biogenesis factor 3)

Gene

• Entrez ID: 8504
• Gene name: Peroxisomal biogenesis factor 3
• Gene symbol: PEX3
• Synonyms (NCBI Gene): PBD10A, PBD10B, TRG18
• Chromosome: 6
• Chromosome location: 6q24.2
• Summary: The product of this gene is involved in peroxisome biosynthesis and integrity. It assembles membrane vesicles before the matrix proteins are translocated. Peroxins (PEXs) are proteins that are essential for the assembly of functional peroxisomes. The pero

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs41285015	A>G	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs147556993	C>A,T	Pathogenic, benign	Coding sequence variant, synonymous variant, stop gained
rs200807211	A>G	Conflicting-interpretations-of-pathogenicity	Intron variant
rs201179294	C>T	Pathogenic	Coding sequence variant, stop gained
rs267608193	T>G	Pathogenic	Intron variant
rs752904598	G>A	Pathogenic	Splice acceptor variant
rs758701470	G>A	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs1057523689	G>A	Likely-pathogenic	Coding sequence variant, missense variant
rs1562653663	TAAG>-	Pathogenic	Splice donor variant, coding sequence variant, intron variant
rs1562654527	G>A	Likely-pathogenic	Missense variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT238882	hsa-miR-1183	PAR-CLIP	22100165
MIRT446022	hsa-miR-4301	PAR-CLIP	22100165
MIRT238876	hsa-miR-20b-3p	PAR-CLIP	22100165
MIRT238900	hsa-miR-4703-3p	PAR-CLIP	22100165
MIRT238889	hsa-miR-3156-3p	PAR-CLIP	22100165
MIRT238882	hsa-miR-1183	PAR-CLIP	22100165
MIRT446022	hsa-miR-4301	PAR-CLIP	22100165
MIRT238876	hsa-miR-20b-3p	PAR-CLIP	22100165
MIRT238900	hsa-miR-4703-3p	PAR-CLIP	22100165
MIRT238889	hsa-miR-3156-3p	PAR-CLIP	22100165
MIRT238882	hsa-miR-1183	PAR-CLIP	22100165
MIRT446022	hsa-miR-4301	PAR-CLIP	22100165
MIRT238876	hsa-miR-20b-3p	PAR-CLIP	22100165
MIRT238900	hsa-miR-4703-3p	PAR-CLIP	22100165
MIRT238889	hsa-miR-3156-3p	PAR-CLIP	22100165
MIRT238882	hsa-miR-1183	PAR-CLIP	22100165
MIRT446022	hsa-miR-4301	PAR-CLIP	22100165
MIRT238876	hsa-miR-20b-3p	PAR-CLIP	22100165
MIRT238900	hsa-miR-4703-3p	PAR-CLIP	22100165
MIRT238889	hsa-miR-3156-3p	PAR-CLIP	22100165
MIRT2066019	hsa-miR-3161	CLIP-seq
MIRT2293651	hsa-miR-223	CLIP-seq
MIRT2293652	hsa-miR-3135b	CLIP-seq
MIRT2293653	hsa-miR-3928	CLIP-seq
MIRT2293654	hsa-miR-4328	CLIP-seq
MIRT2293655	hsa-miR-4716-5p	CLIP-seq
MIRT2293656	hsa-miR-4803	CLIP-seq
MIRT2293657	hsa-miR-765	CLIP-seq
MIRT2456269	hsa-miR-29a	CLIP-seq
MIRT2456270	hsa-miR-29b	CLIP-seq
MIRT2456271	hsa-miR-29c	CLIP-seq
MIRT2456272	hsa-miR-3065-5p	CLIP-seq
MIRT2456273	hsa-miR-3613-3p	CLIP-seq
MIRT2456269	hsa-miR-29a	CLIP-seq
MIRT2456270	hsa-miR-29b	CLIP-seq
MIRT2456271	hsa-miR-29c	CLIP-seq
MIRT2456272	hsa-miR-3065-5p	CLIP-seq
MIRT2456273	hsa-miR-3613-3p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	10704444, 11883941, 12096124, 16189514, 16280322, 18174172, 19715730, 21102411, 25416956, 25502805, 27107012, 28514442, 29997244, 31467278, 31515488, 32296183, 32814053, 33961781, 35271311, 37398436, 38225382
GO:0005654	Component	Nucleoplasm	IDA
GO:0005777	Component	Peroxisome	IDA	9922452
GO:0005777	Component	Peroxisome	IEA
GO:0005777	Component	Peroxisome	IMP	12924628
GO:0005778	Component	Peroxisomal membrane	HDA	21525035
GO:0005778	Component	Peroxisomal membrane	IBA
GO:0005778	Component	Peroxisomal membrane	IDA	9657383, 10430017
GO:0005778	Component	Peroxisomal membrane	IEA
GO:0005778	Component	Peroxisomal membrane	TAS
GO:0005783	Component	Endoplasmic reticulum	IDA	19479899, 21768384
GO:0007031	Process	Peroxisome organization	IEA
GO:0007031	Process	Peroxisome organization	IMP	10958759, 12924628, 18174172, 19479899
GO:0008289	Function	Lipid binding	IDA	19715730
GO:0016020	Component	Membrane	HDA	19946888
GO:0016020	Component	Membrane	IEA
GO:0030674	Function	Protein-macromolecule adaptor activity	IBA
GO:0032991	Component	Protein-containing complex	IDA	18174172
GO:0032994	Component	Protein-lipid complex	IDA	19715730
GO:0045046	Process	Protein import into peroxisome membrane	IBA
GO:0045046	Process	Protein import into peroxisome membrane	IMP	15007061

Other IDs

• MIM: 603164
• HGNC: 8858
• e!Ensembl: ENSG00000034693

Protein

• UniProt ID: P56589
• Protein name: Peroxisomal biogenesis factor 3 (Peroxin-3) (Peroxisomal assembly protein PEX3)
• Protein function: Involved in peroxisome biosynthesis and integrity. Assembles membrane vesicles before the matrix proteins are translocated. As a docking factor for PEX19, is necessary for the import of peroxisomal membrane proteins in the peroxisomes. {ECO:0000
• PDB: 3AJB, 3MK4
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF04882	Peroxin-3	7 → 100	Peroxin-3	Family
  PF04882	Peroxin-3	94 → 364	Peroxin-3	Family

• Tissue specificity: TISSUE SPECIFICITY: Found in all examined tissues.
• Sequence:

  MLRSVWNFLKRHKKKCIFLGTVLGGVYILGKYGQKKIREIQEREAAEYIAQARRQYHFES
  NQRTCNMTVLSMLPTLREALMQQLNSESLTALLKNRPSNKLEIWEDLKIISFTRSTVAVY
  STCMLVVLLRVQLNIIGGYIYLDNAAVGKNGTTILAPPDVQQQYLSSIQHLLGDGLTELI
  TVIKQAVQKVLGSVSLKHSLSLLDLEQKLKEIRNLVEQHKSSSWINKDGSKPLLCHYMMP
  DEETPLAVQACGLSPRDITTIKLLNETRDMLESPDFSTVLNTCLNRGFSRLLDNMAEFFR
  PTEQDLQHGNSMNSLSSVSLPLAKIIPIVNGQIHSVCSETPSHFVQDLLTMEQVKDFAAN
  VYEAFSTPQQLEK

• Sequence length: 373

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Peroxisome biogenesis disorder	Pathogenic; Likely pathogenic	rs1243154971, rs2537199055, rs2537193194	RCV003479376 RCV003155779 RCV003230991	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Peroxisome biogenesis disorder 10A (Zellweger)	Likely pathogenic; Pathogenic	rs1473197986, rs62641230, rs150841396, rs1411756701, rs752904598, rs267608193, rs748689554	RCV001376168 RCV000006997 RCV003388694 RCV003990120 RCV004559642 RCV000006998 RCV001250050	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Peroxisome biogenesis disorder 10B	Pathogenic	rs201179294	RCV000444777	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Peroxisome biogenesis disorder 1A (Zellweger)	Pathogenic	rs267608193	RCV000778169	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PEX3-related disorder	Likely pathogenic; Pathogenic	rs752904598	RCV003396309	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Hepatocellular carcinoma	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PEROXISOME BIOGENESIS DISORDER 10A	—	CTD, ClinVar, Disgenet, GenCC, HPO CTD, ClinVar, Disgenet, GenCC, HPO CTD, ClinVar, Disgenet, GenCC, HPO CTD, ClinVar, Disgenet, GenCC, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PEROXISOME BIOGENESIS DISORDER 1A	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PEROXISOME BIOGENESIS DISORDERS	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
ZELLWEGER SPECTRUM DISORDERS	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Addison Disease	Addison`s Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Adrenoleukodystrophy, Neonatal	Adrenoleukodystrophy	ORPHANET_DG			★☆☆☆☆ Found in Text Mining only
Blepharoptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma Ovarian Epithelial	Epithelial ovarian carcinoma	Pubtator	33676525	Associate	★☆☆☆☆ Found in Text Mining only
Cardiomyopathies	Cardiomyopathy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cataract	Cataract	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Epicanthus	Congenital Epicanthus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cryptorchidism	Cryptorchidism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Developmental regression	Developmental regression	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Facial paralysis	Facial paralysis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glaucoma	Glaucoma	HPO_DG			★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydronephrosis	Hydronephrosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hydrops Fetalis	Hydrops Fetalis	BEFREE	20033294		★☆☆☆☆ Found in Text Mining only
Hypertrophy of clitoris	Hypertrophy Of Clitoris	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypospadias	Hypospadias	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ichthyoses	Ichthyosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	HPO_DG			★☆☆☆☆ Found in Text Mining only
Infantile Refsum disease	Refsum Disease	Orphanet			★☆☆☆☆ Found in Text Mining only
Infantile Refsum Disease (disorder)	Infantile Refsum Disease	BEFREE	23245813		★☆☆☆☆ Found in Text Mining only
Infantile Refsum Disease (disorder)	Infantile Refsum Disease	ORPHANET_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	BEFREE	28673549		★☆☆☆☆ Found in Text Mining only
Liver Failure	Liver failure	HPO_DG			★☆☆☆☆ Found in Text Mining only
Long narrow head	Dolichocephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Macrocephaly	Macrocephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malabsorption Syndrome	Malabsorption Syndrome	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malformations of Cortical Development, Group II	Malformation of cortical development	HPO_DG			★☆☆☆☆ Found in Text Mining only
melanoma	Melanoma	BEFREE	30622661		★☆☆☆☆ Found in Text Mining only
Melanoma	Melanoma	Pubtator	30622661, 37616051	Associate	★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Multicystic Dysplastic Kidney	Multicystic renal dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neonatal adrenoleukodystrophy	Adrenoleukodystrophy	Orphanet			★☆☆☆☆ Found in Text Mining only
Nephrocalcinosis	Nephrocalcinosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neurogenic Urinary Bladder	Neurogenic Urinary Bladder	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nyctalopia	Nyctalopia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nystagmus	Nystagmus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Optic Atrophy	Optic Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Osteochondrodysplasias	Osteochondrodysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
PEROXISOME BIOGENESIS DISORDER 10A (ZELLWEGER)	Zellweger Syndrome	UNIPROT_DG	10848631, 10958759		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PEROXISOME BIOGENESIS DISORDER 10A (ZELLWEGER)	Zellweger Syndrome	GENOMICS_ENGLAND_DG	10968777, 20033294, 24357685, 25655951, 27604308, 28673549		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PEROXISOME BIOGENESIS DISORDER 10A (ZELLWEGER)	Zellweger Syndrome	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PEROXISOME BIOGENESIS DISORDER 10A (ZELLWEGER)	Zellweger Syndrome	CTD_human_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
PEROXISOME BIOGENESIS DISORDER 10B	Zellweger Syndrome	GENOMICS_ENGLAND_DG	24357685		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PEROXISOME BIOGENESIS DISORDER 10B	Zellweger Syndrome	UNIPROT_DG	27557811		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PEROXISOME BIOGENESIS DISORDER 10B	Zellweger Syndrome	CLINVAR_DG	27557811		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PEROXISOME BIOGENESIS DISORDER 10B	Zellweger Syndrome	CTD_human_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PEROXISOME BIOGENESIS DISORDER 1A (ZELLWEGER)	Zellweger Syndrome	CLINVAR_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
PEROXISOME BIOGENESIS DISORDER 1A (ZELLWEGER)	Zellweger Syndrome	GENOMICS_ENGLAND_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Peroxisome biogenesis disorders	Zellweger Syndrome	BEFREE	10679269, 10968777, 23245813		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Peroxisome biogenesis disorders	Zellweger Syndrome	CTD_human_DG	10942428		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Peroxisome biogenesis disorders	Zellweger Syndrome	GENOMICS_ENGLAND_DG	27604308		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Polymicrogyria	Polymicrogyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Posterior embryotoxon	Posterior embryotoxon	HPO_DG			★☆☆☆☆ Found in Text Mining only
Posteriorly rotated ear	Posteriorly Rotated Ear	HPO_DG			★☆☆☆☆ Found in Text Mining only
Profound global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ptosis	Ptosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Rod-Cone Dystrophy	Rod-cone dystrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Sensorineural Hearing Loss (disorder)	Hearing Loss	HPO_DG			★☆☆☆☆ Found in Text Mining only
Skeletal dysplasia	Skeletal Dysplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Spastic Paraplegia	Spastic Paraplegia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ventricular Septal Defects	Ventricular septal defect	HPO_DG			★☆☆☆☆ Found in Text Mining only
Zellweger Spectrum	Zellweger Syndrome	CTD_human_DG	10942428		★☆☆☆☆ Found in Text Mining only
Zellweger Syndrome	Zellweger Syndrome	BEFREE	10871277, 10942428, 10958759, 10968777, 19479899, 23245813		★☆☆☆☆ Found in Text Mining only
Zellweger Syndrome	Zellweger Syndrome	CTD_human_DG	10942428		★☆☆☆☆ Found in Text Mining only
Zellweger syndrome	Zellweger Syndrome	Orphanet			★☆☆☆☆ Found in Text Mining only
Zellweger Syndrome	Zellweger Syndrome	GENOMICS_ENGLAND_DG			★☆☆☆☆ Found in Text Mining only
Zellweger-Like Syndrome	Zellweger-Like Syndrome	CTD_human_DG	10942428		★☆☆☆☆ Found in Text Mining only