Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	5193
Gene name	Peroxisomal biogenesis factor 12
Gene symbol	PEX12
Synonyms (NCBI Gene)	PAF-3PBD3A
Chromosome	17
Chromosome location	17q12
Summary	This gene belongs to the peroxin-12 family. Peroxins (PEXs) are proteins that are essential for the assembly of functional peroxisomes. The peroxisome biogenesis disorders (PBDs) are a group of genetically heterogeneous autosomal recessive, lethal disease

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SNP ID	Visualize variation	Clinical significance	Consequence
rs28936697	G>A	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs28936698	T>A	Pathogenic	Missense variant, coding sequence variant
rs61752097	TG>-	Pathogenic	Frameshift variant, coding sequence variant
rs61752100	CTTT>-	Likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant
rs61752102	TGT>-	Likely-pathogenic, pathogenic	Inframe deletion, coding sequence variant
rs61752103	G>A,C	Pathogenic	Stop gained, missense variant, coding sequence variant
rs61752105	G>A	Pathogenic	Stop gained, coding sequence variant
rs61752106	G>A,T	Likely-pathogenic, pathogenic	Stop gained, missense variant, coding sequence variant
rs61752107	->GGCA	Pathogenic-likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant
rs61752108	->A	Likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant
rs61752112	G>A	Pathogenic, uncertain-significance	Missense variant, coding sequence variant
rs62642859	TAAC>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs104894616	T>A	Pathogenic	Stop gained, coding sequence variant
rs139417458	C>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, missense variant
rs144259891	C>A,T	Pathogenic	Splice donor variant
rs150186509	C>T	Conflicting-interpretations-of-pathogenicity	Missense variant, coding sequence variant
rs187526749	T>G	Conflicting-interpretations-of-pathogenicity, likely-pathogenic	Splice acceptor variant
rs200283718	C>T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Synonymous variant, coding sequence variant
rs200641558	A>G	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Synonymous variant, coding sequence variant
rs267608184	TGT>-	Likely-pathogenic	Inframe deletion, coding sequence variant
rs398123301	AG>-	Pathogenic	Frameshift variant, coding sequence variant
rs398123302	G>-	Likely-pathogenic, pathogenic	Frameshift variant, coding sequence variant
rs747099919	C>T	Likely-pathogenic	Coding sequence variant, stop gained
rs749650201	CCAG>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs751058068	GAA>-	Likely-pathogenic, uncertain-significance	Coding sequence variant, inframe deletion
rs754193088	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs758132842	T>C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant
rs760739894	G>A,T	Likely-pathogenic, uncertain-significance	Coding sequence variant, stop gained, missense variant
rs765404768	A>T	Likely-pathogenic	Coding sequence variant, stop gained
rs767447750	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs776731688	G>A	Pathogenic, likely-pathogenic	Stop gained, coding sequence variant
rs786205502	G>A,T	Likely-pathogenic	Missense variant, coding sequence variant, stop gained
rs886041458	CTGG>-,CTGGCTGG	Pathogenic	Coding sequence variant, frameshift variant
rs888633730	G>A	Likely-pathogenic	Coding sequence variant, stop gained
rs904972651	C>T	Likely-pathogenic	Splice donor variant
rs941358133	G>T	Likely-pathogenic	Coding sequence variant, stop gained
rs1057519507	->TA	Pathogenic	Frameshift variant, coding sequence variant
rs1199283977	G>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1214971073	GAGTA>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1238451790	->GTGCTACC	Likely-pathogenic	Inframe indel, coding sequence variant, stop gained
rs1555549754	G>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1555549769	CACT>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1555549841	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1555549855	G>A	Likely-pathogenic	Stop gained, coding sequence variant
rs1555549876	GA>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1555549902	A>T	Likely-pathogenic	Splice donor variant
rs1555549909	AT>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1555549923	TA>-	Likely-pathogenic	Frameshift variant, initiator codon variant, 5 prime UTR variant
rs1567730901	CGGGAAGAAG>-	Likely-pathogenic	Frameshift variant, coding sequence variant
rs1567731767	A>C	Pathogenic	Stop gained, coding sequence variant

129

Show/Hide all (129)

miRTarBase ID	miRNA	Experiments	Reference
MIRT726974	hsa-miR-15a-5p	HITS-CLIP	22473208
MIRT726975	hsa-miR-15b-5p	HITS-CLIP	22473208
MIRT726973	hsa-miR-16-5p	HITS-CLIP	22473208
MIRT726972	hsa-miR-195-5p	HITS-CLIP	22473208
MIRT1225448	hsa-miR-1208	CLIP-seq
MIRT1225449	hsa-miR-1237	CLIP-seq
MIRT1225450	hsa-miR-1248	CLIP-seq
MIRT1225451	hsa-miR-1273e	CLIP-seq
MIRT1225452	hsa-miR-141	CLIP-seq
MIRT1225453	hsa-miR-15a	CLIP-seq
MIRT1225454	hsa-miR-15b	CLIP-seq
MIRT1225455	hsa-miR-16	CLIP-seq
MIRT1225456	hsa-miR-1910	CLIP-seq
MIRT1225457	hsa-miR-194	CLIP-seq
MIRT1225458	hsa-miR-195	CLIP-seq
MIRT1225459	hsa-miR-200a	CLIP-seq
MIRT1225460	hsa-miR-2278	CLIP-seq
MIRT1225461	hsa-miR-296-3p	CLIP-seq
MIRT1225462	hsa-miR-3117-5p	CLIP-seq
MIRT1225463	hsa-miR-3133	CLIP-seq
MIRT1225464	hsa-miR-3607-3p	CLIP-seq
MIRT1225465	hsa-miR-3686	CLIP-seq
MIRT1225466	hsa-miR-424	CLIP-seq
MIRT1225467	hsa-miR-425	CLIP-seq
MIRT1225468	hsa-miR-4317	CLIP-seq
MIRT1225469	hsa-miR-433	CLIP-seq
MIRT1225470	hsa-miR-4477a	CLIP-seq
MIRT1225471	hsa-miR-4511	CLIP-seq
MIRT1225472	hsa-miR-4524	CLIP-seq
MIRT1225473	hsa-miR-4690-5p	CLIP-seq
MIRT1225474	hsa-miR-4760-3p	CLIP-seq
MIRT1225475	hsa-miR-4766-3p	CLIP-seq
MIRT1225476	hsa-miR-4777-5p	CLIP-seq
MIRT1225477	hsa-miR-491-3p	CLIP-seq
MIRT1225478	hsa-miR-497	CLIP-seq
MIRT1225479	hsa-miR-503	CLIP-seq
MIRT1225480	hsa-miR-518d-5p	CLIP-seq
MIRT1225481	hsa-miR-519b-5p	CLIP-seq
MIRT1225482	hsa-miR-519c-5p	CLIP-seq
MIRT1225483	hsa-miR-520c-5p	CLIP-seq
MIRT1225484	hsa-miR-526a	CLIP-seq
MIRT1225485	hsa-miR-548p	CLIP-seq
MIRT1225486	hsa-miR-646	CLIP-seq
MIRT1225453	hsa-miR-15a	CLIP-seq
MIRT1225454	hsa-miR-15b	CLIP-seq
MIRT1225455	hsa-miR-16	CLIP-seq
MIRT1225458	hsa-miR-195	CLIP-seq
MIRT1225462	hsa-miR-3117-5p	CLIP-seq
MIRT1225466	hsa-miR-424	CLIP-seq
MIRT1225472	hsa-miR-4524	CLIP-seq
MIRT1225475	hsa-miR-4766-3p	CLIP-seq
MIRT2065827	hsa-miR-495	CLIP-seq
MIRT1225478	hsa-miR-497	CLIP-seq
MIRT1225479	hsa-miR-503	CLIP-seq
MIRT1225485	hsa-miR-548p	CLIP-seq
MIRT2065828	hsa-miR-576-3p	CLIP-seq
MIRT1225486	hsa-miR-646	CLIP-seq
MIRT2065829	hsa-miR-668	CLIP-seq
MIRT2293566	hsa-miR-1185	CLIP-seq
MIRT2293567	hsa-miR-1294	CLIP-seq
MIRT1225452	hsa-miR-141	CLIP-seq
MIRT1225453	hsa-miR-15a	CLIP-seq
MIRT1225454	hsa-miR-15b	CLIP-seq
MIRT1225455	hsa-miR-16	CLIP-seq
MIRT1225457	hsa-miR-194	CLIP-seq
MIRT1225458	hsa-miR-195	CLIP-seq
MIRT1225459	hsa-miR-200a	CLIP-seq
MIRT1225462	hsa-miR-3117-5p	CLIP-seq
MIRT1225463	hsa-miR-3133	CLIP-seq
MIRT2293568	hsa-miR-323-3p	CLIP-seq
MIRT2293569	hsa-miR-3605-5p	CLIP-seq
MIRT2293570	hsa-miR-3617	CLIP-seq
MIRT2293571	hsa-miR-3679-5p	CLIP-seq
MIRT1225466	hsa-miR-424	CLIP-seq
MIRT2293572	hsa-miR-4267	CLIP-seq
MIRT2293573	hsa-miR-4316	CLIP-seq
MIRT1225470	hsa-miR-4477a	CLIP-seq
MIRT2293574	hsa-miR-4504	CLIP-seq
MIRT1225471	hsa-miR-4511	CLIP-seq
MIRT1225472	hsa-miR-4524	CLIP-seq
MIRT2293575	hsa-miR-4677-3p	CLIP-seq
MIRT2293576	hsa-miR-4679	CLIP-seq
MIRT1225475	hsa-miR-4766-3p	CLIP-seq
MIRT1225478	hsa-miR-497	CLIP-seq
MIRT1225479	hsa-miR-503	CLIP-seq
MIRT2293577	hsa-miR-542-3p	CLIP-seq
MIRT1225485	hsa-miR-548p	CLIP-seq
MIRT2293578	hsa-miR-641	CLIP-seq
MIRT1225486	hsa-miR-646	CLIP-seq
MIRT1225448	hsa-miR-1208	CLIP-seq
MIRT2591605	hsa-miR-1264	CLIP-seq
MIRT1225453	hsa-miR-15a	CLIP-seq
MIRT1225454	hsa-miR-15b	CLIP-seq
MIRT1225455	hsa-miR-16	CLIP-seq
MIRT1225458	hsa-miR-195	CLIP-seq
MIRT1225462	hsa-miR-3117-5p	CLIP-seq
MIRT1225463	hsa-miR-3133	CLIP-seq
MIRT2591606	hsa-miR-3160-5p	CLIP-seq
MIRT1225466	hsa-miR-424	CLIP-seq
MIRT2591607	hsa-miR-4263	CLIP-seq
MIRT2591608	hsa-miR-431	CLIP-seq
MIRT1225470	hsa-miR-4477a	CLIP-seq
MIRT1225471	hsa-miR-4511	CLIP-seq
MIRT2591609	hsa-miR-4514	CLIP-seq
MIRT1225472	hsa-miR-4524	CLIP-seq
MIRT2591610	hsa-miR-4692	CLIP-seq
MIRT2591611	hsa-miR-4736	CLIP-seq
MIRT1225475	hsa-miR-4766-3p	CLIP-seq
MIRT2591612	hsa-miR-4799-5p	CLIP-seq
MIRT2591613	hsa-miR-490-3p	CLIP-seq
MIRT1225477	hsa-miR-491-3p	CLIP-seq
MIRT1225478	hsa-miR-497	CLIP-seq
MIRT1225479	hsa-miR-503	CLIP-seq
MIRT1225485	hsa-miR-548p	CLIP-seq
MIRT2591614	hsa-miR-576-5p	CLIP-seq
MIRT2591615	hsa-miR-629	CLIP-seq
MIRT1225486	hsa-miR-646	CLIP-seq
MIRT2591616	hsa-miR-649	CLIP-seq
MIRT2591617	hsa-miR-940	CLIP-seq
MIRT2591605	hsa-miR-1264	CLIP-seq
MIRT2591606	hsa-miR-3160-5p	CLIP-seq
MIRT2591607	hsa-miR-4263	CLIP-seq
MIRT2591608	hsa-miR-431	CLIP-seq
MIRT2591609	hsa-miR-4514	CLIP-seq
MIRT2591610	hsa-miR-4692	CLIP-seq
MIRT2591611	hsa-miR-4736	CLIP-seq
MIRT2591612	hsa-miR-4799-5p	CLIP-seq
MIRT2591614	hsa-miR-576-5p	CLIP-seq
MIRT2591617	hsa-miR-940	CLIP-seq

Show/Hide all (48)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000209	Process	Protein polyubiquitination	IDA	24662292
GO:0000209	Process	Protein polyubiquitination	IDA	24662292
GO:0000425	Process	Pexophagy	IDA	26344566, 27597759
GO:0004842	Function	Ubiquitin-protein transferase activity	IBA
GO:0005515	Function	Protein binding	IPI	10562279, 10704444, 10837480, 12096124, 32296183
GO:0005777	Component	Peroxisome	IDA	9922452
GO:0005777	Component	Peroxisome	IEA
GO:0005778	Component	Peroxisomal membrane	HDA	21525035
GO:0005778	Component	Peroxisomal membrane	IBA
GO:0005778	Component	Peroxisomal membrane	IDA	9922452, 12751901
GO:0005778	Component	Peroxisomal membrane	IDA	9090384, 9354782
GO:0005778	Component	Peroxisomal membrane	IEA
GO:0005778	Component	Peroxisomal membrane	TAS	10562279
GO:0005829	Component	Cytosol	TAS
GO:0006513	Process	Protein monoubiquitination	IBA
GO:0006513	Process	Protein monoubiquitination	IDA	27597759
GO:0006513	Process	Protein monoubiquitination	ISS	35768507
GO:0006515	Process	Protein quality control for misfolded or incompletely synthesized proteins	ISS	35768507
GO:0006515	Process	Protein quality control for misfolded or incompletely synthesized proteins	ISS	35768507
GO:0006625	Process	Protein targeting to peroxisome	NAS	12096124
GO:0007031	Process	Peroxisome organization	IDA	9354782
GO:0007031	Process	Peroxisome organization	IEA
GO:0007031	Process	Peroxisome organization	IMP	17534573
GO:0008270	Function	Zinc ion binding	IEA
GO:0008270	Function	Zinc ion binding	IMP	10562279
GO:0008320	Function	Protein transmembrane transporter activity	ISS	35768507
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016558	Process	Protein import into peroxisome matrix	IBA
GO:0016558	Process	Protein import into peroxisome matrix	IDA	21976670
GO:0016558	Process	Protein import into peroxisome matrix	IEA
GO:0016558	Process	Protein import into peroxisome matrix	IMP	9090384, 10562279
GO:0016558	Process	Protein import into peroxisome matrix	NAS	12456682
GO:0016562	Process	Protein import into peroxisome matrix, receptor recycling	IDA	16854980, 19208625
GO:0016562	Process	Protein import into peroxisome matrix, receptor recycling	IDA	24662292
GO:0016567	Process	Protein ubiquitination	IEA
GO:0034614	Process	Cellular response to reactive oxygen species	IDA	26344566
GO:0034614	Process	Cellular response to reactive oxygen species	IDA	26344566
GO:0043161	Process	Proteasome-mediated ubiquitin-dependent protein catabolic process	ISS	35768507
GO:0043161	Process	Proteasome-mediated ubiquitin-dependent protein catabolic process	ISS	35768507
GO:0043335	Process	Protein unfolding	IDA	16854980
GO:0044721	Process	Protein import into peroxisome matrix, substrate release	IDA	26344566
GO:0044721	Process	Protein import into peroxisome matrix, substrate release	ISS	35768507
GO:0044721	Process	Protein import into peroxisome matrix, substrate release	ISS	35768507
GO:0046872	Function	Metal ion binding	IEA
GO:0061630	Function	Ubiquitin protein ligase activity	IDA	24662292
GO:1990429	Component	Peroxisomal importomer complex	IBA
GO:1990757	Function	Ubiquitin ligase activator activity	IDA	24662292

MIM	HGNC	e!Ensembl
601758	8854	ENSG00000108733

O00623

Protein name

Peroxisome assembly protein 12 (Peroxin-12) (Peroxisome assembly factor 3) (PAF-3)

Protein function

Component of a retrotranslocation channel required for peroxisome organization by mediating export of the PEX5 receptor from peroxisomes to the cytosol, thereby promoting PEX5 recycling (PubMed:24662292, PubMed:9354782, PubMed:9632816). The retr

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF04757	Pex2_Pex12	26 → 267	Pex2 / Pex12 amino terminal region	Family

Sequence

MAEHGAHFTAASVADDQPSIFEVVAQDSLMTAVRPALQHVVKVLAESNPTHYGFLWRWFD
EIFTLLDLLLQQHYLSRTSASFSENFYGLKRIVMGDTHKSQRLASAGLPKQQLWKSIMFL
VLLPYLKVKLEKLVSSLREEDEYSIHPPSSRWKRFYRAFLAAYPFVNMAWEGWFLVQQLR
YILGKAQHHSPLLRLAGVQLGRLTVQDIQALEHKPAKASMMQQPARSVSEKINSALKKAV
GGVALSLSTGLSVGVFFLQFLDWWYSSENQETIKSLTALPTPPPPVHLDYNSDSPLLPKM
KTVCPLCRKTRVNDTVLATSGYVFCYRCVFHYVRSHQACPITGYPTEVQHLIKLYSPEN

Sequence length

359

Interactions

View interactions

	KEGG		Reactome
	Peroxisome		E3 ubiquitin ligases ubiquitinate target proteins Peroxisomal protein import Class I peroxisomal membrane protein import

656

Show/Hide Causal Diseases (6)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Acute myeloid leukemia	Likely pathogenic; Pathogenic	rs144259891	RCV005900642
Peroxisomal biogenesis disorder 3b	Pathogenic; Likely pathogenic	rs61752103, rs28936697, rs61752097, rs28936698	RCV000032926 RCV000008217 RCV000008218 RCV000008220
Peroxisome biogenesis disorder	Likely pathogenic; Pathogenic	rs867245161, rs61752109, rs61752103, rs28936697, rs61752107, rs144259891, rs61752102, rs61752100, rs764657253, rs61752108, rs61752106, rs1567730901, rs398123301	RCV004017827 RCV005636691 RCV001193474 RCV002281700 RCV000781710 RCV000589854 RCV003403180 RCV000781708 RCV003226365 RCV001174916 RCV000781711 RCV000781713 RCV000586945
Peroxisome biogenesis disorder 3A (Zellweger)	Pathogenic; Likely pathogenic	rs2142228734, rs2072781707, rs2142228928, rs867245161, rs2142228982, rs1056238409, rs61752099, rs2142231201, rs2142231221, rs61752101, rs144259891, rs2072782816, rs2142231111, rs1429126106, rs923109489 View all (80 more)	RCV001377791 RCV001381260 RCV001380807 RCV001381697 RCV001383266 RCV001388910 RCV001382682 RCV001381954 RCV001390348 RCV001844387 RCV001965297 RCV001939441 RCV001931308 RCV001932496 RCV001898428 RCV002037812 RCV001918071 RCV001957889 RCV001877826 RCV001951022 RCV001935814 RCV001974575 RCV001918534 RCV003050466 RCV003064438 RCV000675037 RCV002654874 RCV002667002 RCV002797324 RCV002806700 RCV002842557 RCV002838593 RCV002867852 RCV002928936 RCV003006038 RCV002991867 RCV003046219 RCV003053594 RCV003024618 RCV000008215 RCV000008216 RCV000625796 RCV003476796 RCV003476797 RCV003476798 RCV003476799 RCV003476800 RCV003535211 RCV003536789 RCV003649728 RCV003651116 RCV003651186 RCV003651174 RCV003651238 RCV003652366 RCV003653826 RCV003651457 RCV003828630 RCV003859839 RCV004574502 RCV004574503 RCV004574504 RCV000410995 RCV000410147 RCV000412365 RCV000416562 RCV000502221 RCV000674819 RCV000665252 RCV000667563 RCV000674917 RCV000668008 RCV000672949 RCV000666724 RCV000666102 RCV000666647 RCV000673039 RCV000668380 RCV000668677 RCV000665795 RCV000667506 RCV000674616 RCV000671104 RCV000672791 RCV000674189 RCV000669254 RCV000671389 RCV000666766 RCV000664813 RCV000670011 RCV000669057 RCV000671986 RCV000669146 RCV001050835 RCV001206889 RCV000412263 RCV000669619
Peroxisome biogenesis disorder type 3B	Likely pathogenic; Pathogenic	rs923109489, rs776731688, rs2509168104, rs61752103, rs28936697, rs2072790040, rs61752107, rs62642859, rs144259891, rs61752102, rs760739894, rs61752100, rs941358133, rs749650201, rs1555549841 View all (23 more)	RCV005016764 RCV000675037 RCV005008774 RCV000666018 RCV005394138 RCV005012965 RCV000409475 RCV000412130 RCV002505997 RCV000670939 RCV000674819 RCV000665252 RCV000667563 RCV000674917 RCV000668008 RCV000672949 RCV000666724 RCV000666102 RCV000666647 RCV000673039 RCV000668380 RCV000668677 RCV000665795 RCV000667506 RCV000674616 RCV000671104 RCV000672791 RCV000674189 RCV000669254 RCV000671389 RCV000666766 RCV000664813 RCV000670011 RCV000669057 RCV000671986 RCV000669146 RCV000410739 RCV000669619
PEX12-related disorder	Likely pathogenic; Pathogenic	rs776731688, rs2509169676, rs61752107, rs61752100, rs1555549855, rs398123301, rs398123302	RCV004552945 RCV004554281 RCV003335311 RCV003336090 RCV004547837 RCV004739344 RCV004724797

Show/Hide Unknown Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Familial cancer of breast	Conflicting classifications of pathogenicity	rs138731505	RCV005886193
Peroxisome biogenesis disorder 1A (Zellweger)	Uncertain significance; Benign; Likely benign	rs767207001, rs35050283, rs886052825, rs147182821, rs3031851, rs886052830	RCV000260746 RCV000264131 RCV000286510 RCV000337909 RCV000372610 RCV000271524
Sarcoma	Conflicting classifications of pathogenicity	rs138731505	RCV005886194
Thyroid cancer, nonmedullary, 1	Conflicting classifications of pathogenicity	rs138731505	RCV005886195

Show/Hide Text Mining Associations (3)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Neurologic Manifestations	Associate	10562279
Peroxisome biogenesis disorders	Associate	19105186, 9792857
Zellweger Syndrome	Associate	10562279, 19105186, 26319495, 9792857

PEX12 (peroxisomal biogenesis factor 12)