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	116442
Gene name	RAB39B, member RAS oncogene family
Gene symbol	RAB39B
Synonyms (NCBI Gene)	BGMRMRX72WSMNWSNXLID72
Chromosome	X
Chromosome location	Xq28
Summary	This gene encodes a member of the Rab family of proteins. Rab proteins are small GTPases that are involved in vesicular trafficking. Mutations in this gene are associated with X-linked cognitive disability. [provided by RefSeq, Aug 2013]

Show/Hide all (6)

SNP ID	Visualize variation	Clinical significance	Consequence
rs267606995	G>T	Pathogenic	Coding sequence variant, stop gained
rs587776734	C>T	Pathogenic	Splice donor variant
rs587777874	G>T	Pathogenic	Missense variant, coding sequence variant
rs864309527	C>T	Pathogenic	Missense variant, coding sequence variant
rs1557314191	C>A	Pathogenic	Stop gained, coding sequence variant
rs1557314544	A>G	Pathogenic	Initiator codon variant, missense variant

144

Show/Hide all (144)

miRTarBase ID	miRNA	Experiments	Reference
MIRT024007	hsa-miR-1-3p	Microarray	18668037
MIRT555004	hsa-miR-101-3p	PAR-CLIP	21572407
MIRT555004	hsa-miR-101-3p	PAR-CLIP	21572407
MIRT555003	hsa-miR-144-3p	PAR-CLIP	21572407
MIRT555002	hsa-miR-548n	PAR-CLIP	21572407
MIRT555001	hsa-miR-548l	PAR-CLIP	21572407
MIRT554999	hsa-miR-3609	PAR-CLIP	21572407
MIRT555000	hsa-miR-548ah-5p	PAR-CLIP	21572407
MIRT554998	hsa-miR-3529-3p	PAR-CLIP	21572407
MIRT554996	hsa-miR-4778-5p	PAR-CLIP	21572407
MIRT554997	hsa-miR-520g-3p	PAR-CLIP	21572407
MIRT554995	hsa-miR-520h	PAR-CLIP	21572407
MIRT554994	hsa-miR-3065-5p	PAR-CLIP	21572407
MIRT554992	hsa-miR-5003-5p	PAR-CLIP	21572407
MIRT554993	hsa-miR-4766-5p	PAR-CLIP	21572407
MIRT554990	hsa-miR-3928-3p	PAR-CLIP	21572407
MIRT554991	hsa-miR-6124	PAR-CLIP	21572407
MIRT554989	hsa-let-7f-2-3p	PAR-CLIP	21572407
MIRT554988	hsa-miR-1185-1-3p	PAR-CLIP	21572407
MIRT554987	hsa-miR-1185-2-3p	PAR-CLIP	21572407
MIRT554986	hsa-miR-3915	PAR-CLIP	21572407
MIRT555004	hsa-miR-101-3p	PAR-CLIP	21572407
MIRT555004	hsa-miR-101-3p	PAR-CLIP	21572407
MIRT555003	hsa-miR-144-3p	PAR-CLIP	21572407
MIRT555002	hsa-miR-548n	PAR-CLIP	21572407
MIRT555001	hsa-miR-548l	PAR-CLIP	21572407
MIRT554999	hsa-miR-3609	PAR-CLIP	21572407
MIRT555000	hsa-miR-548ah-5p	PAR-CLIP	21572407
MIRT554998	hsa-miR-3529-3p	PAR-CLIP	21572407
MIRT554996	hsa-miR-4778-5p	PAR-CLIP	21572407
MIRT554997	hsa-miR-520g-3p	PAR-CLIP	21572407
MIRT554995	hsa-miR-520h	PAR-CLIP	21572407
MIRT554994	hsa-miR-3065-5p	PAR-CLIP	21572407
MIRT554992	hsa-miR-5003-5p	PAR-CLIP	21572407
MIRT554993	hsa-miR-4766-5p	PAR-CLIP	21572407
MIRT554990	hsa-miR-3928-3p	PAR-CLIP	21572407
MIRT554991	hsa-miR-6124	PAR-CLIP	21572407
MIRT554989	hsa-let-7f-2-3p	PAR-CLIP	21572407
MIRT554988	hsa-miR-1185-1-3p	PAR-CLIP	21572407
MIRT554987	hsa-miR-1185-2-3p	PAR-CLIP	21572407
MIRT554986	hsa-miR-3915	PAR-CLIP	21572407
MIRT1283886	hsa-miR-101	CLIP-seq
MIRT1283887	hsa-miR-1229	CLIP-seq
MIRT1283888	hsa-miR-1243	CLIP-seq
MIRT1283889	hsa-miR-1261	CLIP-seq
MIRT1283890	hsa-miR-129-5p	CLIP-seq
MIRT1283891	hsa-miR-1297	CLIP-seq
MIRT1283892	hsa-miR-144	CLIP-seq
MIRT1283893	hsa-miR-148a	CLIP-seq
MIRT1283894	hsa-miR-148b	CLIP-seq
MIRT1283895	hsa-miR-152	CLIP-seq
MIRT1283896	hsa-miR-1909	CLIP-seq
MIRT1283897	hsa-miR-26a	CLIP-seq
MIRT1283898	hsa-miR-26b	CLIP-seq
MIRT1283899	hsa-miR-3124-3p	CLIP-seq
MIRT1283900	hsa-miR-320e	CLIP-seq
MIRT1283901	hsa-miR-3545-3p	CLIP-seq
MIRT1283902	hsa-miR-3622a-3p	CLIP-seq
MIRT1283903	hsa-miR-3622b-3p	CLIP-seq
MIRT1283904	hsa-miR-3928	CLIP-seq
MIRT1283905	hsa-miR-4251	CLIP-seq
MIRT1283906	hsa-miR-4277	CLIP-seq
MIRT1283907	hsa-miR-4324	CLIP-seq
MIRT1283908	hsa-miR-433	CLIP-seq
MIRT1283909	hsa-miR-4446-3p	CLIP-seq
MIRT1283910	hsa-miR-4465	CLIP-seq
MIRT1283911	hsa-miR-4656	CLIP-seq
MIRT1283912	hsa-miR-4729	CLIP-seq
MIRT1283913	hsa-miR-4753-3p	CLIP-seq
MIRT1283914	hsa-miR-4768-5p	CLIP-seq
MIRT1283915	hsa-miR-4775	CLIP-seq
MIRT1283916	hsa-miR-520g	CLIP-seq
MIRT1283917	hsa-miR-548ah	CLIP-seq
MIRT1283918	hsa-miR-550b	CLIP-seq
MIRT1283919	hsa-miR-580	CLIP-seq
MIRT1283920	hsa-miR-582-5p	CLIP-seq
MIRT1283921	hsa-miR-587	CLIP-seq
MIRT1283922	hsa-miR-590-3p	CLIP-seq
MIRT1283923	hsa-miR-630	CLIP-seq
MIRT1283924	hsa-miR-9	CLIP-seq
MIRT2084190	hsa-miR-125a-5p	CLIP-seq
MIRT2084191	hsa-miR-125b	CLIP-seq
MIRT2084192	hsa-miR-1272	CLIP-seq
MIRT2084193	hsa-miR-1321	CLIP-seq
MIRT2084194	hsa-miR-1322	CLIP-seq
MIRT2084195	hsa-miR-3152-5p	CLIP-seq
MIRT1283901	hsa-miR-3545-3p	CLIP-seq
MIRT1283902	hsa-miR-3622a-3p	CLIP-seq
MIRT1283903	hsa-miR-3622b-3p	CLIP-seq
MIRT2084196	hsa-miR-375	CLIP-seq
MIRT1283905	hsa-miR-4251	CLIP-seq
MIRT2084197	hsa-miR-4269	CLIP-seq
MIRT2084198	hsa-miR-4319	CLIP-seq
MIRT1283907	hsa-miR-4324	CLIP-seq
MIRT2084199	hsa-miR-4419a	CLIP-seq
MIRT2084200	hsa-miR-4503	CLIP-seq
MIRT2084201	hsa-miR-4510	CLIP-seq
MIRT2084202	hsa-miR-4514	CLIP-seq
MIRT2084203	hsa-miR-4692	CLIP-seq
MIRT2084204	hsa-miR-4739	CLIP-seq
MIRT2084205	hsa-miR-4742-5p	CLIP-seq
MIRT1283913	hsa-miR-4753-3p	CLIP-seq
MIRT2084206	hsa-miR-4756-5p	CLIP-seq
MIRT2084207	hsa-miR-4774-3p	CLIP-seq
MIRT2084208	hsa-miR-4777-5p	CLIP-seq
MIRT2084209	hsa-miR-518d-5p	CLIP-seq
MIRT2084210	hsa-miR-519b-5p	CLIP-seq
MIRT2084211	hsa-miR-519c-5p	CLIP-seq
MIRT2084212	hsa-miR-520c-5p	CLIP-seq
MIRT1283916	hsa-miR-520g	CLIP-seq
MIRT2084213	hsa-miR-526a	CLIP-seq
MIRT1283919	hsa-miR-580	CLIP-seq
MIRT1283920	hsa-miR-582-5p	CLIP-seq
MIRT2309444	hsa-miR-2277-3p	CLIP-seq
MIRT2309445	hsa-miR-3660	CLIP-seq
MIRT2309446	hsa-miR-4526	CLIP-seq
MIRT1283912	hsa-miR-4729	CLIP-seq
MIRT2309447	hsa-miR-664	CLIP-seq
MIRT2606144	hsa-miR-1206	CLIP-seq
MIRT2606145	hsa-miR-1225-5p	CLIP-seq
MIRT2606146	hsa-miR-1324	CLIP-seq
MIRT2606147	hsa-miR-183	CLIP-seq
MIRT2606148	hsa-miR-3132	CLIP-seq
MIRT2606149	hsa-miR-3166	CLIP-seq
MIRT2606150	hsa-miR-3529	CLIP-seq
MIRT2606151	hsa-miR-3688-3p	CLIP-seq
MIRT2606152	hsa-miR-379	CLIP-seq
MIRT2606153	hsa-miR-4261	CLIP-seq
MIRT2606154	hsa-miR-4302	CLIP-seq
MIRT2606155	hsa-miR-4457	CLIP-seq
MIRT2606156	hsa-miR-4522	CLIP-seq
MIRT2606157	hsa-miR-4762-3p	CLIP-seq
MIRT2606158	hsa-miR-513b	CLIP-seq
MIRT2606159	hsa-miR-552	CLIP-seq
MIRT2606160	hsa-miR-579	CLIP-seq
MIRT2606161	hsa-miR-609	CLIP-seq
MIRT2606162	hsa-miR-635	CLIP-seq
MIRT2606163	hsa-miR-873	CLIP-seq
MIRT2606144	hsa-miR-1206	CLIP-seq
MIRT2606155	hsa-miR-4457	CLIP-seq
MIRT2606157	hsa-miR-4762-3p	CLIP-seq
MIRT2606158	hsa-miR-513b	CLIP-seq
MIRT2606160	hsa-miR-579	CLIP-seq
MIRT2606161	hsa-miR-609	CLIP-seq

Show/Hide all (31)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0000421	Component	Autophagosome membrane	IEA
GO:0003924	Function	GTPase activity	IBA
GO:0003924	Function	GTPase activity	IEA
GO:0003925	Function	G protein activity	IEA
GO:0005515	Function	Protein binding	IPI	24705354, 25416956, 27103069, 31515488, 32296183, 37821429
GO:0005525	Function	GTP binding	IBA
GO:0005525	Function	GTP binding	IEA
GO:0005764	Component	Lysosome	IEA
GO:0005794	Component	Golgi apparatus	IDA	20159109, 24006491
GO:0005794	Component	Golgi apparatus	IEA
GO:0005886	Component	Plasma membrane	IEA
GO:0006914	Process	Autophagy	IEA
GO:0010506	Process	Regulation of autophagy	IMP	27103069
GO:0015031	Process	Protein transport	IEA
GO:0016020	Component	Membrane	IEA
GO:0016192	Process	Vesicle-mediated transport	IBA
GO:0016192	Process	Vesicle-mediated transport	IEA
GO:0016192	Process	Vesicle-mediated transport	ISS
GO:0016787	Function	Hydrolase activity	IEA
GO:0030659	Component	Cytoplasmic vesicle membrane	IEA
GO:0031410	Component	Cytoplasmic vesicle	IEA
GO:0031489	Function	Myosin V binding	IBA
GO:0031489	Function	Myosin V binding	IPI	24006491
GO:0031982	Component	Vesicle	IDA	24006491
GO:0032482	Process	Rab protein signal transduction	IEA
GO:0043005	Component	Neuron projection	IDA	24006491
GO:0046872	Function	Metal ion binding	IEA
GO:0050808	Process	Synapse organization	IEA
GO:0050808	Process	Synapse organization	ISS
GO:0120281	Component	Autolysosome membrane	IEA

MIM	HGNC	e!Ensembl
300774	16499	ENSG00000155961

Q96DA2

Protein name

Ras-related protein Rab-39B (EC 3.6.5.2)

Protein function

The small GTPases Rab are key regulators of intracellular membrane trafficking, from the formation of transport vesicles to their fusion with membranes. Rabs cycle between an inactive GDP-bound form and an active GTP-bound form that is able to r

PDB

6S5F

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00071	Ras	10 → 173	Ras family	Domain

Tissue specificity

TISSUE SPECIFICITY: Highly expressed in the brain. {ECO:0000269|PubMed:20159109}.

Sequence

MEAIWLYQFRLIVIGDSTVGKSCLIRRFTEGRFAQVSDPTVGVDFFSRLVEIEPGKRIKL
QIWDTAGQERFRSITRAYYRNSVGGLLLFDITNRRSFQNVHEWLEETKVHVQPYQIVFVL
VGHKCDLDTQRQVTRHEAEKLAAAYGMKYIETSARDAINVEKAFTDLTRDIYELVKRGEI
TIQEGWEGVKSGFVPNVVHSSEEVVKSERRCLC

Sequence length

213

Interactions

View interactions

	KEGG		Reactome
	Autophagy - animal Amyotrophic lateral sclerosis Pathways of neurodegeneration - multiple diseases		RAB geranylgeranylation RAB GEFs exchange GTP for GDP on RABs

Show/Hide Causal Diseases (5)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Developmental disorder	Likely pathogenic	rs2124126312	RCV001843763
Early-onset parkinsonism-intellectual disability syndrome	Pathogenic	rs587777874, rs864309527	RCV000150034 RCV000207511
Intellectual disability, X-linked 72	Likely pathogenic; Pathogenic	rs2124130091, rs587776734, rs267606995, rs1557314191	RCV004813203 RCV000011288 RCV000011289 RCV000503295
Neurodevelopmental disorder	Likely pathogenic	rs1569561107	RCV000782058
Parkinson disease, X-linked dominant	Pathogenic	rs864309527	RCV000202604

Show/Hide Unknown Diseases (2)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Unknown Diseases with uncertain, conflicting, or no pathogenic evidence in ClinVar
Non-syndromic X-linked intellectual disability	Uncertain significance	rs1057515830, rs1057515834, rs1057515828, rs1057515832	RCV000403266 RCV000364495 RCV000384887 RCV000304388
RAB39B-related disorder	Benign; Likely benign; Conflicting classifications of pathogenicity	rs782592713, rs369970931, rs377143859, rs181687825	RCV004553651 RCV004552977 RCV004547890 RCV004547899

Show/Hide Text Mining Associations (22)

Disease Name	Relationship Type	References
Associations from Text MiningDisease associations identified through Pubtator
Aphasia	Associate	35088096
Autism Spectrum Disorder	Associate	29152164
Autistic Disorder	Associate	29152164, 32873259
Cafe au Lait Spots	Associate	32873259
Chromosome Xq28 Duplication Syndrome	Associate	35595445
Cognition Disorders	Stimulate	25927380
Genetic Diseases Inborn	Associate	29257243
Intellectual Disability	Associate	25434005, 27459931, 29152164, 32873259, 35088096
Lewy Body Disease	Associate	25434005, 32762091
Megalencephaly	Associate	29152164
Neoplasms Germ Cell and Embryonal	Associate	17970049
Nerve Degeneration	Associate	25434005
Neurodegenerative Diseases	Associate	25434005, 32762091
Neurofibromatosis 1	Associate	32873259
Neurofibromatosis Noonan syndrome	Associate	29152164
Pancreatic Neoplasms	Associate	32702921
Parkinson Disease	Associate	25434005, 29128816, 32762091, 32873259, 34247111, 35088096
Parkinson Disease 12	Associate	29128816, 32762091
Parkinson Disease Secondary	Associate	27459931, 35088096
Parkinsonism early onset with mental retardation	Associate	35088096
Progressive hearing loss stapes fixation	Associate	32873259
Retrograde Degeneration	Associate	32762091

RAB39B (RAB39B, member RAS oncogene family)