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Aliases for RAB39B Gene

Aliases for RAB39B Gene

  • RAB39B, Member RAS Oncogene Family 2 3 5
  • Waisman Syndrome 2 3
  • Waisman Syndrome (Basal Ganglion Disorder With Mental Retardation) 3
  • Mental Retardation, X-Linked 72 2
  • Ras-Related Protein Rab-39B 3
  • MRX72 3
  • BGMR 3
  • WSMN 3
  • WSN 3

External Ids for RAB39B Gene

Previous HGNC Symbols for RAB39B Gene

  • MRX72
  • WSN

Previous GeneCards Identifiers for RAB39B Gene

  • GC00U991112
  • GC0XM150941
  • GC0XM152004
  • GC0XM152909
  • GC0XM152900
  • GC0XM154051
  • GC0XM154140
  • GC0XM154487
  • GC0XM143031

Summaries for RAB39B Gene

Entrez Gene Summary for RAB39B Gene

  • 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]

GeneCards Summary for RAB39B Gene

RAB39B (RAB39B, Member RAS Oncogene Family) is a Protein Coding gene. Diseases associated with RAB39B include Waisman Syndrome and X-Linked Non-Specific Intellectual Disability. Among its related pathways are Metabolism of proteins and RAB GEFs exchange GTP for GDP on RABs. Gene Ontology (GO) annotations related to this gene include GTP binding and myosin V binding. An important paralog of this gene is RAB39A.

UniProtKB/Swiss-Prot for RAB39B Gene

  • Small GTPases Rab involved in autophagy (PubMed:27103069). 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 recruit to membranes different sets of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion (PubMed:27103069). May regulate the homeostasis of SNCA/alpha-synuclein. Together with PICK1 proposed to ensure selectively GRIA2 exit from the endoplasmic reticulum to the Golgi and to regulate AMPAR compostion at the post-synapses and thus synaptic transmission (By similarity).

Gene Wiki entry for RAB39B Gene

Additional gene information for RAB39B Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for RAB39B Gene

Genomics for RAB39B Gene

GeneHancer (GH) Regulatory Elements for RAB39B Gene

Promoters and enhancers for RAB39B Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XJ155262 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 650.7 +0.6 646 2.3 SIN3A ZNF2 YY1 GLIS2 ZNF143 FOS RUNX3 YY2 KDM1A ZNF785 RAB39B TMLHE ENSG00000224978
GH0XJ155215 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 0.2 +47.7 47721 3.1 PKNOX1 ATF1 ARNT DMAP1 YY1 ETS1 POLR2B GLIS2 ZNF143 FOS VBP1 F8A1 DKC1 WASH6P SNORA70 ENSG00000224978 RAB39B
GH0XJ155242 Enhancer 0.5 Ensembl 0.3 +22.0 22004 0.8 SCRT1 SP1 SCRT2 ATF7 SPI1 MTCP1 RAB39B ENSG00000224978
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around RAB39B on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the RAB39B gene promoter:
  • C/EBPalpha
  • CUTL1
  • p53
  • IRF-7A
  • HTF
  • POU2F2C
  • POU2F2B
  • POU2F2 (Oct-2.1)
  • POU2F2
  • POU2F1a

Genomic Locations for RAB39B Gene

Genomic Locations for RAB39B Gene
chrX:155,258,234-155,264,589
(GRCh38/hg38)
Size:
6,356 bases
Orientation:
Minus strand
chrX:154,487,526-154,493,874
(GRCh37/hg19)
Size:
6,349 bases
Orientation:
Minus strand

Genomic View for RAB39B Gene

Genes around RAB39B on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
RAB39B Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for RAB39B Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for RAB39B Gene

Proteins for RAB39B Gene

  • Protein details for RAB39B Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96DA2-RB39B_HUMAN
    Recommended name:
    Ras-related protein Rab-39B
    Protein Accession:
    Q96DA2
    Secondary Accessions:
    • Q5JT79
    • Q8NEX3

    Protein attributes for RAB39B Gene

    Size:
    213 amino acids
    Molecular mass:
    24622 Da
    Quaternary structure:
    • Interacts (in GTP-bound form) with PICK1 (via PDZ domain); a PICK1 homodimer may allow simultaneous association of RAB39B and GRIA2 to PICK1 which is involved in GRIA2 trafficking.

neXtProt entry for RAB39B Gene

Post-translational modifications for RAB39B Gene

  • Ubiquitination at posLast=140140
  • Modification sites at PhosphoSitePlus

Other Protein References for RAB39B Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for RAB39B Gene

Domains & Families for RAB39B Gene

Gene Families for RAB39B Gene

HGNC:
Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for RAB39B Gene

Suggested Antigen Peptide Sequences for RAB39B Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q96DA2

UniProtKB/Swiss-Prot:

RB39B_HUMAN :
  • Belongs to the small GTPase superfamily. Rab family.
Family:
  • Belongs to the small GTPase superfamily. Rab family.
genes like me logo Genes that share domains with RAB39B: view

Function for RAB39B Gene

Molecular function for RAB39B Gene

UniProtKB/Swiss-Prot Function:
Small GTPases Rab involved in autophagy (PubMed:27103069). 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 recruit to membranes different sets of downstream effectors directly responsible for vesicle formation, movement, tethering and fusion (PubMed:27103069). May regulate the homeostasis of SNCA/alpha-synuclein. Together with PICK1 proposed to ensure selectively GRIA2 exit from the endoplasmic reticulum to the Golgi and to regulate AMPAR compostion at the post-synapses and thus synaptic transmission (By similarity).

Gene Ontology (GO) - Molecular Function for RAB39B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003924 GTPase activity IEA --
GO:0005515 protein binding IPI 24705354
GO:0005525 GTP binding IEA --
GO:0031489 myosin V binding IPI 24006491
genes like me logo Genes that share ontologies with RAB39B: view
genes like me logo Genes that share phenotypes with RAB39B: view

Human Phenotype Ontology for RAB39B Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Model Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Animal Models , Transcription Factor Targets and HOMER Transcription for RAB39B Gene

Localization for RAB39B Gene

Subcellular locations from UniProtKB/Swiss-Prot for RAB39B Gene

Cell membrane; Lipid-anchor; Cytoplasmic side. Cytoplasmic vesicle membrane; Lipid-anchor; Cytoplasmic side. Golgi apparatus. Note=Partial colocalization with markers that cycle from the cell surface to the trans-Golgi network. {ECO:0000250 UniProtKB:Q8BHC1}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for RAB39B gene
Compartment Confidence
golgi apparatus 5
plasma membrane 3
cytosol 3
nucleus 2
mitochondrion 1
peroxisome 1

Gene Ontology (GO) - Cellular Components for RAB39B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000139 Golgi membrane IBA --
GO:0005622 intracellular IDA --
GO:0005794 Golgi apparatus IDA,IEA 20159109
GO:0005886 plasma membrane IEA --
GO:0012505 endomembrane system IBA --
genes like me logo Genes that share ontologies with RAB39B: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for RAB39B Gene

Pathways & Interactions for RAB39B Gene

genes like me logo Genes that share pathways with RAB39B: view

Gene Ontology (GO) - Biological Process for RAB39B Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006886 intracellular protein transport IBA --
GO:0006914 autophagy IEA --
GO:0010506 regulation of autophagy IMP 27103069
GO:0015031 protein transport IEA --
GO:0016192 vesicle-mediated transport IEA,ISS --
genes like me logo Genes that share ontologies with RAB39B: view

No data available for SIGNOR curated interactions for RAB39B Gene

Drugs & Compounds for RAB39B Gene

No Compound Related Data Available

Transcripts for RAB39B Gene

mRNA/cDNA for RAB39B Gene

(1) REFSEQ mRNAs :
(4) Additional mRNA sequences :
(67) Selected AceView cDNA sequences:
(1) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for RAB39B Gene

RAB39B, member RAS oncogene family:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for RAB39B Gene

No ASD Table

Relevant External Links for RAB39B Gene

GeneLoc Exon Structure for
RAB39B
ECgene alternative splicing isoforms for
RAB39B

Expression for RAB39B Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for RAB39B Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for RAB39B Gene

This gene is overexpressed in Brain - Frontal Cortex (BA9) (x4.5) and Brain - Anterior cingulate cortex (BA24) (x4.0).

Protein differential expression in normal tissues from HIPED for RAB39B Gene

This gene is overexpressed in Brain (33.0), Frontal cortex (10.4), Fetal Brain (7.0), and Retina (6.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for RAB39B Gene



Protein tissue co-expression partners for RAB39B Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of RAB39B Gene:

RAB39B

SOURCE GeneReport for Unigene cluster for RAB39B Gene:

Hs.632832

mRNA Expression by UniProt/SwissProt for RAB39B Gene:

Q96DA2-RB39B_HUMAN
Tissue specificity: Highly expressed in the brain.

Evidence on tissue expression from TISSUES for RAB39B Gene

  • Nervous system(4.6)
  • Pancreas(4.1)

Phenotype-based relationships between genes and organs from Gene ORGANizer for RAB39B Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • digestive
  • integumentary
  • nervous
  • reproductive
  • respiratory
  • skeletal muscle
  • skeleton
  • urinary
Regions:
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • nose
  • outer ear
  • salivary gland
  • skull
  • tooth
Thorax:
  • diaphragm
  • lung
  • rib
  • rib cage
Pelvis:
  • pelvis
  • testicle
  • urinary bladder
Limb:
  • ankle
  • digit
  • elbow
  • finger
  • foot
  • hand
  • hip
  • knee
  • lower limb
  • shoulder
  • toe
  • upper limb
  • wrist
General:
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with RAB39B: view

Orthologs for RAB39B Gene

This gene was present in the common ancestor of animals.

Orthologs for RAB39B Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia RAB39B 34 33
  • 100 (n)
OneToOne
mouse
(Mus musculus)
Mammalia Rab39b 16 34 33
  • 97.65 (n)
cow
(Bos Taurus)
Mammalia RAB39B 34 33
  • 94.52 (n)
OneToOne
dog
(Canis familiaris)
Mammalia RAB39B 34 33
  • 94.1 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia RAB39B 34
  • 89 (a)
OneToOne
chicken
(Gallus gallus)
Aves RAB39B 33
  • 84.35 (n)
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100486510 33
  • 78.25 (n)
Str.13291 33
zebrafish
(Danio rerio)
Actinopterygii rab39b 34
  • 90 (a)
OneToMany
tmem230 34 33
  • 75.43 (n)
OneToMany
Dr.29085 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP000433 33
  • 59.47 (n)
fruit fly
(Drosophila melanogaster)
Insecta Rab39 34 33
  • 57.28 (n)
OneToMany
worm
(Caenorhabditis elegans)
Secernentea rab-39 34 33
  • 54.79 (n)
OneToMany
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 59 (a)
OneToMany
Cin.5228 33
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.5228 33
Species where no ortholog for RAB39B was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • lizard (Anolis carolinensis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • platypus (Ornithorhynchus anatinus)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for RAB39B Gene

ENSEMBL:
Gene Tree for RAB39B (if available)
TreeFam:
Gene Tree for RAB39B (if available)
Aminode:
Evolutionary constrained regions (ECRs) for RAB39B: view image

Paralogs for RAB39B Gene

Variants for RAB39B Gene

Sequence variations from dbSNP and Humsavar for RAB39B Gene

SNP ID Clin Chr 0X pos Variation AA Info Type
rs1057515827 uncertain-significance, Non-syndromic X-linked intellectual disability 155,258,703(-) G/A 3_prime_UTR_variant
rs1057515828 uncertain-significance, Non-syndromic X-linked intellectual disability 155,258,847(-) TTTGTTTGT/TTTGT 3_prime_UTR_variant
rs1057515829 uncertain-significance, Non-syndromic X-linked intellectual disability 155,259,075(-) T/C 3_prime_UTR_variant
rs1057515830 uncertain-significance, Non-syndromic X-linked intellectual disability 155,259,182(-) TTTTTTTTTTT/TTTTTTTTTT/TTTTTTTTTTTT 3_prime_UTR_variant
rs1057515831 uncertain-significance, Non-syndromic X-linked intellectual disability 155,259,375(-) A/C 3_prime_UTR_variant

Structural Variations from Database of Genomic Variants (DGV) for RAB39B Gene

Variant ID Type Subtype PubMed ID
esv29972 CNV gain 17803354
esv33784 CNV gain+loss 17666407

Variation tolerance for RAB39B Gene

Residual Variation Intolerance Score: 32.1% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for RAB39B Gene

Human Gene Mutation Database (HGMD)
RAB39B
SNPedia medical, phenotypic, and genealogical associations of SNPs for
RAB39B

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RAB39B Gene

Disorders for RAB39B Gene

MalaCards: The human disease database

(11) MalaCards diseases for RAB39B Gene - From: HGMD, OMIM, ClinVar, GTR, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
waisman syndrome
  • wsmn
x-linked non-specific intellectual disability
  • x-linked non-syndromic intellectual disability
chromosome xq28 duplication syndrome
early-onset parkinson's disease
  • early-onset parkinson disease
non-syndromic x-linked intellectual disability
  • non-specific x-linked mental retardation
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

RB39B_HUMAN
  • Mental retardation, X-linked 72 (MRX72) [MIM:300271]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. Intellectual deficiency is the only primary symptom of non-syndromic X-linked mental retardation, while syndromic mental retardation presents with associated physical, neurological and/or psychiatric manifestations. MRX72 patients can manifest autism spectrum disorder, seizures and macrocephaly as additional features. {ECO:0000269 PubMed:20159109}. Note=The disease is caused by mutations affecting the gene represented in this entry.
  • Waisman syndrome (WSMN) [MIM:311510]: A neurologic disorder characterized by delayed psychomotor development, intellectual disability, and early-onset Parkinson disease. {ECO:0000269 PubMed:25434005, ECO:0000269 PubMed:26399558, ECO:0000269 PubMed:27066548}. Note=The disease is caused by mutations affecting the gene represented in this entry. Its association with Parkinson disease is however unclear (PubMed:26739247, PubMed:27459931). According to a number of studies, variations affecting this gene are not a frequent cause of Parkinson disease, suggesting that RAB39B does not play a major role in Parkinson disease etiology (PubMed:26739247, PubMed:27459931). {ECO:0000269 PubMed:26739247, ECO:0000269 PubMed:27459931}.

Additional Disease Information for RAB39B

genes like me logo Genes that share disorders with RAB39B: view

No data available for Genatlas for RAB39B Gene

Publications for RAB39B Gene

  1. Mutations in RAB39B cause X-linked intellectual disability and early-onset Parkinson disease with α-synuclein pathology. (PMID: 25434005) Wilson GR … Lockhart PJ (American journal of human genetics 2014) 2 3 4 58
  2. Mutations in the small GTPase gene RAB39B are responsible for X-linked mental retardation associated with autism, epilepsy, and macrocephaly. (PMID: 20159109) Giannandrea M … D'Adamo P (American journal of human genetics 2010) 2 3 4 58
  3. Isolation and characterization of a human novel RAB (RAB39B) gene. (PMID: 12438742) Cheng H … Mao Y (Cytogenetic and genome research 2002) 2 3 4 58
  4. RAB39B gene mutations are not a common cause of Parkinson's disease or dementia with Lewy bodies. (PMID: 27459931) Hodges K … Lorenzo-Betancor O (Neurobiology of aging 2016) 3 4 58
  5. Loss of C9ORF72 impairs autophagy and synergizes with polyQ Ataxin-2 to induce motor neuron dysfunction and cell death. (PMID: 27103069) Sellier C … Charlet-Berguerand N (The EMBO journal 2016) 3 4 58

Products for RAB39B Gene

Sources for RAB39B Gene

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