ENSG00000141252


Homo sapiens

Features
Gene ID: ENSG00000141252
  
Biological name :VPS53
  
Synonyms : Q5VIR6 / VPS53 / VPS53, GARP complex subunit
  
Possible biological names infered from orthology :
  
Species: Homo sapiens
  
Chr. number: 17
Strand: -1
Band: p13.3
Gene start: 508668
Gene end: 721717
  
Corresponding Affymetrix probe sets: 1557112_a_at (Human Genome U133 Plus 2.0 Array)   1559108_at (Human Genome U133 Plus 2.0 Array)   1559109_a_at (Human Genome U133 Plus 2.0 Array)   219794_at (Human Genome U133 Plus 2.0 Array)   221707_s_at (Human Genome U133 Plus 2.0 Array)   227229_at (Human Genome U133 Plus 2.0 Array)   229653_at (Human Genome U133 Plus 2.0 Array)   235710_at (Human Genome U133 Plus 2.0 Array)   235882_at (Human Genome U133 Plus 2.0 Array)   
  
Cross references: Ensembl peptide - ENSP00000459312
Ensembl peptide - ENSP00000459159
Ensembl peptide - ENSP00000461429
Ensembl peptide - ENSP00000291074
Ensembl peptide - ENSP00000373692
Ensembl peptide - ENSP00000384294
Ensembl peptide - ENSP00000401435
Ensembl peptide - ENSP00000458311
Ensembl peptide - ENSP00000458651
NCBI entrez gene - 55275     See in Manteia.
OMIM - 615850
RefSeq - XM_017024818
RefSeq - NM_001128159
RefSeq - NM_018289
RefSeq - XM_011523953
RefSeq - XM_017024817
RefSeq Peptide - NP_001121631
RefSeq Peptide - NP_060759
swissprot - E7EVT8
swissprot - F6VX93
swissprot - I3L0S6
swissprot - I3L184
swissprot - I3L4P9
swissprot - I3L1W6
swissprot - Q5VIR6
Ensembl - ENSG00000141252
  
Related genetic diseases (OMIM): 615851 - Pontocerebellar hypoplasia, type 2E, 615851
See expression report in BioGPS
See gene description in Wikigenes
See gene description in GeneCards
See co-cited genes in PubMed


Ortholog prediction (from Ensembl)
Ortholog nameID Species
 vps53ENSDARG00000069324Danio rerio
 VPS53ENSGALG00000042071Gallus gallus
 Vps53ENSMUSG00000017288Mus musculus


Paralog prediction (from Ensembl)
Paralog nameIDSimilarity(%)
No match


Protein motifs (from Interpro)
Interpro ID Name
 IPR007234  Vps53-like, N-terminal


Gene Ontology (GO)
TypeGO IDTermEv.Code
 biological_processGO:0007041 lysosomal transport IMP
 biological_processGO:0015031 protein transport IEA
 biological_processGO:0032456 endocytic recycling IMP
 biological_processGO:0042147 retrograde transport, endosome to Golgi IBA
 cellular_componentGO:0000938 GARP complex IDA
 cellular_componentGO:0005768 endosome IEA
 cellular_componentGO:0005794 Golgi apparatus IEA
 cellular_componentGO:0005802 trans-Golgi network IEA
 cellular_componentGO:0005829 cytosol IDA
 cellular_componentGO:0010008 endosome membrane IEA
 cellular_componentGO:0016020 membrane IDA
 cellular_componentGO:0032588 trans-Golgi network membrane TAS
 cellular_componentGO:0048471 perinuclear region of cytoplasm IDA
 cellular_componentGO:0055037 recycling endosome IEA
 cellular_componentGO:1990745 EARP complex IDA
 molecular_functionGO:0005515 protein binding IPI


Pathways (from Reactome)
Pathway description
Retrograde transport at the Trans-Golgi-Network


Phenotype (from MGI, Zfin or HPO)
IDPhenotypeDefinition Genetic BG
 HP:0000007 Autosomal recessive inheritance "A mode of inheritance that is observed for traits related to a gene encoded on one of the autosomes (i.e., the human chromosomes 1-22) in which a trait manifests in homozygotes. In the context of medical genetics, autosomal recessive disorders manifest in homozygotes (with two copies of the mutant allele) or compound heterozygotes (whereby each copy of a gene has a distinct mutant allele)." [HPO:curators]
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 HP:0000253 Microcephaly, progressive "Progressive microcephaly is diagnosed when the head circumference falls progressively behind age- and gender-dependent norms." [HPO:curators]
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 HP:0000737 Irritability 
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 HP:0000939 Osteoporosis "Osteoporosis is a systemic skeletal disease characterized by low bone density and microarchitectural deterioration of bone tissue with a consequent increase in bone fragility. According to the WHO, osteoporosis is characterized by a value of BMD 2.5 standard deviations or more below the young adult mean." [HPO:curators]
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 HP:0001250 Seizures "Seizures are an intermittent `abnormality of the central nervous system` (FMA:HP:0002011) due to a sudden, excessive, disorderly discharge of cerebral neurons and characterized clinically by some combination of disturbance of sensation, loss of consciousness, impairment of psychic function, or convulsive movements." [HPO:probinson]
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 HP:0001263 Developmental retardation "A delay in the achievement of motor or mental milestones manifested prior to age 18 and generally associated with lifelong mental and/or physical impairments." [HPO:curators]
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 HP:0001272 Cerebellar atrophy 
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 HP:0001319 Neonatal hypotonia "Muscular hypotonia (abnormally low muscle tone) manifesting in the neonatal period." [HPO:curators]
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 HP:0001371 Contractures 
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 HP:0002059 Cerebral atrophy 
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 HP:0002079 Hypoplasia of the corpus callosum "Underdevelopment of the corpus callosum." [HPO:curators]
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 HP:0002179 Opisthotonus 
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 HP:0002187 Mental retardation, profound "Severe mental retardation is defined as an intelligence quotient (IQ) below 20." [HPO:curators]
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 HP:0002510 Spastic tetraplegia "Spastic paralysis affecting all four limbs." [HPO:curators]
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 HP:0002650 Scoliosis "The presence of an abnormal lateral curvature of the spine." [HPO:curators]
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 HP:0003593 Early onset 
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 HP:0003676 Progressive disorder 
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 HP:0004322 Decreased body height "A height below that which is expected according to age and gender norms. Although there is no universally accepted definition of short stature, many refer to "short stature" as height more than 2 standard deviations below the mean for age and gender (or below the 3rd percentile for age and gender dependent norms)." [HPO:curators]
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Interacting proteins (from Reactome)
Interactor ID Name Interaction type
 ENSG00000003056 M6PR / P20645 / mannose-6-phosphate receptor, cation dependent  / reaction
 ENSG00000049245 VAMP3 / Q15836 / vesicle associated membrane protein 3  / reaction
 ENSG00000123595 RAB9A / P51151 / RAB9A, member RAS oncogene family  / reaction
 ENSG00000104915 STX10 / O60499 / syntaxin 10  / reaction
 ENSG00000136933 Q7Z6M1 / RABEPK / Rab9 effector protein with kelch motifs  / reaction
 ENSG00000149823 VPS51 / Q9UID3 / VPS51, GARP complex subunit  / complex
 ENSG00000223501 VPS52 / Q8N1B4 / VPS52, GARP complex subunit  / complex
 ENSG00000143952 VPS54 / Q9P1Q0 / VPS54, GARP complex subunit  / complex
 ENSG00000124222 STX16 / O14662 / syntaxin 16  / reaction
 ENSG00000135968 GCC2 / Q8IWJ2 / GRIP and coiled-coil domain containing 2  / reaction
 ENSG00000197081 IGF2R / P11717 / insulin like growth factor 2 receptor  / reaction
 ENSG00000151532 VTI1A / Q96AJ9 / vesicle transport through interaction with t-SNAREs 1A  / reaction






 

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