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This gene encodes for a protein that in yeast forms part of a trimeric vacuolar-protein-sorting complex that is required for retrograde transport of proteins from prevacuoles to the late Golgi compartment. As in yeast, mammalian Vps54 proteins contain a coiled-coil region and dileucine motifs. Alternative splicing results in multiple transcript variants encoding different isoforms [provided by RefSeq, Jul 2008]
VPS54 (VPS54 Subunit Of GARP Complex) is a Protein Coding gene. Diseases associated with VPS54 include Frontotemporal Dementia And/Or Amyotrophic Lateral Sclerosis 3 and Spermatogenic Failure 9. Among its related pathways are Retrograde transport at the Trans-Golgi-Network and Golgi-to-ER retrograde transport. Gene Ontology (GO) annotations related to this gene include syntaxin binding.
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 |
---|---|---|---|---|---|---|---|---|---|---|
GH02J064017 | Promoter/Enhancer | 2.2 | EPDnew Ensembl ENCODE CraniofacialAtlas | 600.7 | +0.5 | 518 | 3.8 | GATAD2A PRDM10 ZNF629 ZNF512 SOX13 IKZF1 NFKBIZ ZNF692 POLR2A BACH1 | VPS54 WDPCP MDH1 ENSG00000225889 piR-54908 UGP2 | |
GH02J063975 | Promoter | 0.6 | EPDnew | 600.3 | +43.8 | 43808 | 0.1 | ZNF316 ZBTB5 NFE2 CC2D1A EMSY | VPS54 piR-58790-002 piR-37663-029 UGP2 | |
GH02J064090 | Promoter | 0.4 | EPDnew | 600.2 | -71.0 | -71030 | 0.1 | RBM22 | lnc-UGP2-3-001 lnc-UGP2-3-002 VPS54 ENSG00000225889 LOC100507006 PELI1 | |
GH02J064004 | Promoter | 0.3 | EPDnew | 600.4 | +15.4 | 15387 | 0.1 | VPS54 piR-50968-062 piR-54908 UGP2 | ||
GH02J063919 | Promoter | 0.3 | EPDnew | 600.2 | +99.5 | 99527 | 0.1 | VPS54 lnc-WDPCP-6 ENSG00000251775 UGP2 |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0005515 | protein binding | IPI | 3172165 |
GO:0019905 | syntaxin binding | IBA | 21873635 |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0000938 | GARP complex | IEA,IDA | 19620288 |
GO:0005654 | nucleoplasm | IDA | -- |
GO:0005794 | Golgi apparatus | IEA,IDA | 15878329 |
GO:0005802 | trans-Golgi network | IMP | 25795912 |
GO:0005829 | cytosol | IEA | -- |
SuperPathway | Contained pathways | ||
---|---|---|---|
1 | Vesicle-mediated transport | ||
2 | Golgi-to-ER retrograde transport | ||
3 | Retrograde transport at the Trans-Golgi-Network |
Symbol | External ID(s) | Details |
---|---|---|
CDK3 | ||
EIPR1 | ||
ENSG00000272822 | ||
STX5 | ||
STX6 |
GO ID | Qualified GO term | Evidence | PubMed IDs |
---|---|---|---|
GO:0006896 | Golgi to vacuole transport | IBA | 21873635 |
GO:0007041 | lysosomal transport | IMP | 25799061 |
GO:0015031 | protein transport | IEA | -- |
GO:0040008 | regulation of growth | IEA | -- |
GO:0042147 | retrograde transport, endosome to Golgi | IEA,IMP | 25799061 |
ExUns: | 1 | ^ | 2 | ^ | 3 | ^ | 4 | ^ | 5 | ^ | 6 | ^ | 7 | ^ | 8 | ^ | 9 | ^ | 10 | ^ | 11 | ^ | 12 | ^ | 13 | ^ | 14a | · | 14b | ^ | 15a | · | 15b | ^ | 16 | ^ | 17 | ^ | 18 | ^ | 19 | ^ | 20 | ^ | 21 | ^ | 22 | ^ | 23a | · | 23b |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
SP1: | - | - | |||||||||||||||||||||||||||||||||||||||||||||||||
SP2: | - | ||||||||||||||||||||||||||||||||||||||||||||||||||
SP3: |
This gene was present in the common ancestor of eukaryotes.
Organism | Taxonomy | Gene | Similarity | Type | Details |
---|---|---|---|---|---|
Chimpanzee (Pan troglodytes) |
Mammalia | VPS54 30 31 |
|
OneToOne | |
Cow (Bos Taurus) |
Mammalia | VPS54 30 31 |
|
OneToOne | |
Dog (Canis familiaris) |
Mammalia | VPS54 30 31 |
|
OneToOne | |
Mouse (Mus musculus) |
Mammalia | Vps54 30 17 31 |
|
OneToOne | |
Oppossum (Monodelphis domestica) |
Mammalia | VPS54 31 |
|
OneToOne | |
Platypus (Ornithorhynchus anatinus) |
Mammalia | VPS54 31 |
|
OneToOne | |
Rat (Rattus norvegicus) |
Mammalia | Vps54 30 |
|
||
Chicken (Gallus gallus) |
Aves | VPS54 30 31 |
|
OneToOne | |
Lizard (Anolis carolinensis) |
Reptilia | VPS54 31 |
|
OneToOne | |
Tropical Clawed Frog (Silurana tropicalis) |
Amphibia | vps54 30 |
|
||
Str.19681 30 |
|
||||
Zebrafish (Danio rerio) |
Actinopterygii | vps54 30 31 |
|
OneToOne | |
Fruit Fly (Drosophila melanogaster) |
Insecta | scat 30 31 |
|
OneToOne | |
African malaria mosquito (Anopheles gambiae) |
Insecta | AgaP_AGAP008353 30 |
|
||
Worm (Caenorhabditis elegans) |
Secernentea | vps-54 30 31 |
|
OneToOne | |
Baker's yeast (Saccharomyces cerevisiae) |
Saccharomycetes | VPS54 33 |
|
|
|
Thale Cress (Arabidopsis thaliana) |
eudicotyledons | VPS54 30 |
|
||
Rice (Oryza sativa) |
Liliopsida | Os04g0212100 30 |
|
||
Sea Squirt (Ciona savignyi) |
Ascidiacea | CSA.1333 31 |
|
OneToOne |
SNP ID | Clinical significance and condition | Chr 02 pos | Variation | AA Info | Type |
---|---|---|---|---|---|
760240 | Benign: not provided | 63,899,588(-) | G/A | INTRON_VARIANT | |
767802 | Benign: not provided | 63,981,790(-) | G/A | SYNONYMOUS_VARIANT | |
775722 | Benign: not provided | 63,933,730(-) | G/C | MISSENSE_VARIANT | |
805793 | Uncertain Significance: Reduced number of teeth | 63,965,958(-) | C/G | MISSENSE_VARIANT | |
808754 | Uncertain Significance: not provided | 63,920,551(-) | G/C | MISSENSE_VARIANT |
Variant ID | Type | Subtype | PubMed ID |
---|---|---|---|
esv2763643 | CNV | gain | 21179565 |
esv3591067 | CNV | loss | 21293372 |
esv3591068 | CNV | loss | 21293372 |
nsv1002209 | CNV | loss | 25217958 |
nsv1013132 | CNV | loss | 25217958 |
nsv521717 | CNV | gain | 19592680 |
nsv582126 | CNV | gain | 21841781 |
nsv582127 | CNV | gain | 21841781 |
nsv7313 | OTHER | inversion | 18451855 |
Disorder | Aliases | PubMed IDs |
---|---|---|
frontotemporal dementia and/or amyotrophic lateral sclerosis 3 |
|
|
spermatogenic failure 9 |
|
|
frontotemporal dementia and/or amyotrophic lateral sclerosis 4 |
|
|
frontotemporal dementia and/or amyotrophic lateral sclerosis 2 |
|
|
amyotrophic lateral sclerosis type 22 |
|
|