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

Gene Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID Entrez Gene ID - the GENE ID in NCBI Gene database.	5192
Gene name Gene Name - the full gene name approved by the HGNC.	Peroxisomal biogenesis factor 10
Gene symbol Gene Symbol - the official gene symbol approved by the HGNC.	PEX10
Synonyms (NCBI Gene) Gene synonyms aliases	NALD, PBD6A, PBD6B, RNF69
Chromosome Chromosome number	1
Chromosome location Chromosomal Location - indicates the cytogenetic location of the gene or region on the chromosome.	1p36.32
Summary Summary of gene provided in NCBI Entrez Gene.	This gene encodes a protein involved in import of peroxisomal matrix proteins. This protein localizes to the peroxisomal membrane. Mutations in this gene result in phenotypes within the Zellweger spectrum of peroxisomal biogenesis disorders, ranging from

Show/Hide all(36)

SNP ID	Visualize variation	Clinical significance	Consequence
rs61750434	G>A	Pathogenic, likely-pathogenic	5 prime UTR variant, non coding transcript variant, coding sequence variant, stop gained
rs61750435	->T	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant, genic downstream transcript variant, downstream transcript variant
rs61752092	G>A,C	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant, missense variant, genic downstream transcript variant, downstream transcript variant
rs61752093	AG>-	Pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant, genic downstream transcript variant, downstream transcript variant
rs61752095	G>C	Pathogenic	Coding sequence variant, non coding transcript variant, missense variant, genic downstream transcript variant, downstream transcript variant
rs62641225	C>A,T	Pathogenic	Coding sequence variant, stop gained, non coding transcript variant, missense variant, genic downstream transcript variant, downstream transcript variant
rs75377471	G>A	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Non coding transcript variant, coding sequence variant, synonymous variant
rs78620392	G>A,T	Uncertain-significance, conflicting-interpretations-of-pathogenicity	Downstream transcript variant, coding sequence variant, missense variant, genic downstream transcript variant, non coding transcript variant
rs140133667	C>T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, genic downstream transcript variant, downstream transcript variant, non coding transcript variant
rs140340426	G>A	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, synonymous variant, 5 prime UTR variant, non coding transcript variant
rs144264865	T>C	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, genic downstream transcript variant, intron variant, downstream transcript variant, missense variant
rs144440263	C>A,T	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, genic downstream transcript variant, downstream transcript variant, non coding transcript variant
rs199934621	C>A,T	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Coding sequence variant, non coding transcript variant, missense variant, genic downstream transcript variant, downstream transcript variant
rs267608183	C>T	Pathogenic	Intron variant, splice donor variant
rs369965266	G>A	Likely-pathogenic	Non coding transcript variant, 5 prime UTR variant, coding sequence variant, stop gained
rs724159999	G>-	Pathogenic	Coding sequence variant, frameshift variant, 5 prime UTR variant, non coding transcript variant
rs724160000	A>G	Uncertain-significance, pathogenic	Non coding transcript variant, missense variant, genic downstream transcript variant, coding sequence variant, downstream transcript variant
rs762783424	G>A,C	Conflicting-interpretations-of-pathogenicity	Non coding transcript variant, 5 prime UTR variant, coding sequence variant, synonymous variant
rs768893724	GCAGCCCCATGG>-	Likely-pathogenic	Inframe indel, coding sequence variant, genic downstream transcript variant, downstream transcript variant, non coding transcript variant, stop gained
rs769251149	C>A,T	Likely-pathogenic	Missense variant, coding sequence variant, genic downstream transcript variant, downstream transcript variant, non coding transcript variant, stop gained
rs775772867	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, synonymous variant, non coding transcript variant, 5 prime UTR variant
rs797044762	->C	Pathogenic	Coding sequence variant, frameshift variant, genic downstream transcript variant, non coding transcript variant, downstream transcript variant
rs867305222	C>T	Likely-pathogenic	Splice acceptor variant
rs869312935	C>G	Pathogenic	Splice donor variant, genic downstream transcript variant, downstream transcript variant
rs878853044	A>-	Pathogenic, likely-pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant, 5 prime UTR variant
rs1325771720	TG>-	Likely-pathogenic	Frameshift variant, genic downstream transcript variant, coding sequence variant, non coding transcript variant, downstream transcript variant
rs1335685844	A>G,T	Likely-pathogenic	Splice donor variant, downstream transcript variant, genic downstream transcript variant
rs1553231739	C>G,T	Likely-pathogenic	Splice donor variant, downstream transcript variant, genic downstream transcript variant
rs1553231783	A>-	Likely-pathogenic	Downstream transcript variant, non coding transcript variant, frameshift variant, coding sequence variant, genic downstream transcript variant
rs1553231787	TC>-	Likely-pathogenic	Downstream transcript variant, non coding transcript variant, frameshift variant, coding sequence variant, genic downstream transcript variant
rs1553231820	C>-	Likely-pathogenic, pathogenic	Downstream transcript variant, non coding transcript variant, frameshift variant, coding sequence variant, genic downstream transcript variant
rs1553231875	TC>-	Likely-pathogenic	Intron variant, downstream transcript variant, frameshift variant, coding sequence variant, genic downstream transcript variant
rs1553231888	CA>GAG	Likely-pathogenic	Intron variant, downstream transcript variant, frameshift variant, coding sequence variant, genic downstream transcript variant
rs1553231896	AG>-	Likely-pathogenic	Intron variant, frameshift variant, coding sequence variant, 3 prime UTR variant
rs1553232077	C>-	Likely-pathogenic	Intron variant, splice donor variant
rs1557910651	G>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, 5 prime UTR variant

Show/Hide all(103)

miRTarBase ID	miRNA	Experiments	Reference
MIRT490349	hsa-miR-4318	PAR-CLIP	23592263
MIRT490350	hsa-miR-3614-5p	PAR-CLIP	23592263
MIRT490348	hsa-miR-4494	PAR-CLIP	23592263
MIRT490347	hsa-miR-499b-5p	PAR-CLIP	23592263
MIRT490346	hsa-miR-4330	PAR-CLIP	23592263
MIRT490345	hsa-miR-7114-5p	PAR-CLIP	23592263
MIRT490343	hsa-miR-4320	PAR-CLIP	23592263
MIRT490344	hsa-miR-3138	PAR-CLIP	23592263
MIRT490342	hsa-miR-4800-5p	PAR-CLIP	23592263
MIRT490341	hsa-miR-4520-3p	PAR-CLIP	23592263
MIRT490340	hsa-miR-450b-3p	PAR-CLIP	23592263
MIRT490339	hsa-miR-769-3p	PAR-CLIP	23592263
MIRT490338	hsa-miR-6728-5p	PAR-CLIP	23592263
MIRT490337	hsa-miR-5089-5p	PAR-CLIP	23592263
MIRT490336	hsa-miR-6513-5p	PAR-CLIP	23592263
MIRT490349	hsa-miR-4318	PAR-CLIP	23592263
MIRT490350	hsa-miR-3614-5p	PAR-CLIP	23592263
MIRT490348	hsa-miR-4494	PAR-CLIP	23592263
MIRT490347	hsa-miR-499b-5p	PAR-CLIP	23592263
MIRT490346	hsa-miR-4330	PAR-CLIP	23592263
MIRT490345	hsa-miR-7114-5p	PAR-CLIP	23592263
MIRT490343	hsa-miR-4320	PAR-CLIP	23592263
MIRT490344	hsa-miR-3138	PAR-CLIP	23592263
MIRT490342	hsa-miR-4800-5p	PAR-CLIP	23592263
MIRT490341	hsa-miR-4520-3p	PAR-CLIP	23592263
MIRT490340	hsa-miR-450b-3p	PAR-CLIP	23592263
MIRT490339	hsa-miR-769-3p	PAR-CLIP	23592263
MIRT490338	hsa-miR-6728-5p	PAR-CLIP	23592263
MIRT490337	hsa-miR-5089-5p	PAR-CLIP	23592263
MIRT490336	hsa-miR-6513-5p	PAR-CLIP	23592263
MIRT1225307	hsa-miR-105	CLIP-seq
MIRT1225308	hsa-miR-1200	CLIP-seq
MIRT1225309	hsa-miR-1321	CLIP-seq
MIRT1225310	hsa-miR-150	CLIP-seq
MIRT1225311	hsa-miR-154	CLIP-seq
MIRT1225312	hsa-miR-1915	CLIP-seq
MIRT1225313	hsa-miR-2052	CLIP-seq
MIRT1225314	hsa-miR-2110	CLIP-seq
MIRT1225315	hsa-miR-2117	CLIP-seq
MIRT1225316	hsa-miR-3150a-3p	CLIP-seq
MIRT1225317	hsa-miR-3160-5p	CLIP-seq
MIRT1225318	hsa-miR-3162-5p	CLIP-seq
MIRT1225319	hsa-miR-3170	CLIP-seq
MIRT1225320	hsa-miR-3183	CLIP-seq
MIRT1225321	hsa-miR-3202	CLIP-seq
MIRT1225322	hsa-miR-326	CLIP-seq
MIRT1225323	hsa-miR-330-5p	CLIP-seq
MIRT1225324	hsa-miR-3672	CLIP-seq
MIRT1225325	hsa-miR-3937	CLIP-seq
MIRT1225326	hsa-miR-4251	CLIP-seq
MIRT1225327	hsa-miR-4260	CLIP-seq
MIRT1225328	hsa-miR-4261	CLIP-seq
MIRT1225329	hsa-miR-4271	CLIP-seq
MIRT1225330	hsa-miR-4273	CLIP-seq
MIRT1225331	hsa-miR-4314	CLIP-seq
MIRT1225332	hsa-miR-4324	CLIP-seq
MIRT1225333	hsa-miR-4328	CLIP-seq
MIRT1225334	hsa-miR-4329	CLIP-seq
MIRT1225335	hsa-miR-4446-3p	CLIP-seq
MIRT1225336	hsa-miR-4652-3p	CLIP-seq
MIRT1225337	hsa-miR-4656	CLIP-seq
MIRT1225338	hsa-miR-4666-5p	CLIP-seq
MIRT1225339	hsa-miR-4680-5p	CLIP-seq
MIRT1225340	hsa-miR-4685-5p	CLIP-seq
MIRT1225341	hsa-miR-4694-3p	CLIP-seq
MIRT1225342	hsa-miR-4713-5p	CLIP-seq
MIRT1225343	hsa-miR-4723-3p	CLIP-seq
MIRT1225344	hsa-miR-4725-3p	CLIP-seq
MIRT1225345	hsa-miR-4726-3p	CLIP-seq
MIRT1225346	hsa-miR-4728-5p	CLIP-seq
MIRT1225347	hsa-miR-4739	CLIP-seq
MIRT1225348	hsa-miR-4747-5p	CLIP-seq
MIRT1225349	hsa-miR-4749-3p	CLIP-seq
MIRT1225350	hsa-miR-4756-5p	CLIP-seq
MIRT1225351	hsa-miR-4768-5p	CLIP-seq
MIRT1225352	hsa-miR-4802-5p	CLIP-seq
MIRT1225353	hsa-miR-490-3p	CLIP-seq
MIRT1225354	hsa-miR-494	CLIP-seq
MIRT1225355	hsa-miR-500a	CLIP-seq
MIRT1225356	hsa-miR-518a-3p	CLIP-seq
MIRT1225357	hsa-miR-518b	CLIP-seq
MIRT1225358	hsa-miR-518c	CLIP-seq
MIRT1225359	hsa-miR-518d-3p	CLIP-seq
MIRT1225360	hsa-miR-518f	CLIP-seq
MIRT1225361	hsa-miR-532-3p	CLIP-seq
MIRT1225362	hsa-miR-539	CLIP-seq
MIRT1225363	hsa-miR-544b	CLIP-seq
MIRT1225364	hsa-miR-570	CLIP-seq
MIRT1225365	hsa-miR-600	CLIP-seq
MIRT1225366	hsa-miR-619	CLIP-seq
MIRT1225367	hsa-miR-657	CLIP-seq
MIRT1225368	hsa-miR-769-5p	CLIP-seq
MIRT1225369	hsa-miR-873	CLIP-seq
MIRT1225370	hsa-miR-875-3p	CLIP-seq
MIRT1225310	hsa-miR-150	CLIP-seq
MIRT1225312	hsa-miR-1915	CLIP-seq
MIRT1225315	hsa-miR-2117	CLIP-seq
MIRT1225330	hsa-miR-4273	CLIP-seq
MIRT1225336	hsa-miR-4652-3p	CLIP-seq
MIRT1225342	hsa-miR-4713-5p	CLIP-seq
MIRT1225345	hsa-miR-4726-3p	CLIP-seq
MIRT1225351	hsa-miR-4768-5p	CLIP-seq
MIRT1225361	hsa-miR-532-3p	CLIP-seq

Show/Hide all(39)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000209	Process	Protein polyubiquitination	IDA	24662292
GO:0000425	Process	Pexophagy	IDA	26344566, 27597759
GO:0005515	Function	Protein binding	IPI	10562279, 10837480
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	9090384, 9922452, 12751901
GO:0005778	Component	Peroxisomal membrane	IDA	9700193
GO:0005778	Component	Peroxisomal membrane	IEA
GO:0005778	Component	Peroxisomal membrane	TAS
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:0007031	Process	Peroxisome organization	IDA	9700193
GO:0007031	Process	Peroxisome organization	IEA
GO:0008270	Function	Zinc ion binding	IEA
GO:0008270	Function	Zinc ion binding	NAS	10862081
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	IDA	9683594
GO:0016558	Process	Protein import into peroxisome matrix	IEA
GO:0016558	Process	Protein import into peroxisome matrix	IMP	10862081
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:0016740	Function	Transferase activity	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: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

MIM	HGNC	e!Ensembl
602859	8851	ENSG00000157911

Protein

UniProt ID

O60683

Protein name

Peroxisome biogenesis factor 10 (EC 2.3.2.27) (Peroxin-10) (Peroxisomal biogenesis factor 10) (Peroxisome assembly protein 10) (RING finger protein 69)

Protein function

E3 ubiquitin-protein ligase 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). The retrotra

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF04757	Pex2_Pex12	18 → 243	Pex2 / Pex12 amino terminal region	Family
PF13920	zf-C3HC4_3	269 → 315		Domain

Sequence

MAPAAASPPEVIRAAQKDEYYRGGLRSAAGGALHSLAGARKWLEWRKEVELLSDVAYFGL
TTLAGYQTLGEEYVSIIQVDPSRIHVPSSLRRGVLVTLHAVLPYLLDKALLPLEQELQAD
PDSGRPLQGSLGPGGRGCSGARRWMRHHTATLTEQQRRALLRAVFVLRQGLACLQRLHVA
WFYIHGVFYHLAKRLTGITYLRVRSLPGEDLRARVSYRLLGVISLLHLVLSMGLQLYGFR
QRQRARKEWRLHRGLSHRRASLEERAVSRNPLCTLCLEERRHPTATPCGHLFCWECITAW
CSSKAECPLCREKFPPQKLIYLRHYR

Sequence length

326

Interactions

View interactions

	KEGG		Reactome
	Peroxisome		E3 ubiquitin ligases ubiquitinate target proteins Peroxisomal protein import

Show/Hide Causal Diseases (1)

Disease merge term	Disease name	dbSNP ID	References
Causal Diseases caused by PATHOGENIC or LIKELY PATHOGENIC variants from ClinVar only
Zellweger Syndrome	Peroxisome biogenesis disorder, peroxisome biogenesis disorder 6a (zellweger), peroxisome biogenesis disorder 6b, peroxisome biogenesis disorder, complementation group 7, Zellweger spectrum disorders	rs61752092, rs1335685844, rs61752093, rs61752095, rs724159999, rs62636524, rs869312935, rs1553231896, rs61750434, rs724160000, rs878853044, rs867305222, rs768893724, rs886041314, rs724160002 View all (11 more)	N/A

Show/Hide Unknown Diseases (1)

Disease merge term	Disease name	Evidence	References	Source
Unknown Includes: (1) ClinVar NON-pathogenic variants (Uncertain, Benign, Conflicting, VUS), (2) GenCC associations, (3) GWAS associations, (4) CBGDA evidence-based associations. NOTE: Diseases with pathogenic evidence are excluded to avoid conflicts.
Ataxia	autosomal recessive ataxia due to PEX10 deficiency	N/A	N/A	GenCC

Show/Hide Text Mining Associations (10)

Disease Name	Relationship Type	References
Associations from Text Mining Disease associations identified through Pubtator
Azoospermia	Associate	24303009
Azoospermia Nonobstructive	Associate	30863997
Down Syndrome	Associate	26911678
Infertility Male	Associate	27232852, 30863997
Oligospermia	Associate	24303009
Peroxisomal Disorders	Associate	28784167
Peroxisome biogenesis disorders	Associate	19105186
Polyneuropathies	Associate	28784167
Spinocerebellar Degenerations	Associate	34234304
Zellweger Syndrome	Associate	19105186, 26319495, 28784167

PEX10 (peroxisomal biogenesis factor 10)