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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 Frontotemporal Dementia And/Or Amyotrophic Lateral Sclerosis 4. Among its related pathways are Vesicle-mediated transport and Golgi-to-ER retrograde transport. Gene Ontology (GO) annotations related to this gene include syntaxin binding.
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 | ||
HIP1 | ||
STX5 |
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 |
---|---|---|---|---|---|
rs1200103911 | Uncertain Significance: not provided | 63,920,551(-) |
G/C NM_016516.3(VPS54):c.1946C>G (p.Thr649Ser) |
MISSENSE | |
rs139082064 | Uncertain Significance: not provided | 63,949,117(-) |
T/C NM_016516.3(VPS54):c.1057A>G (p.Met353Val) |
MISSENSE | |
rs1422204880 | Uncertain Significance: not provided | 63,933,691(-) |
G/C NM_016516.3(VPS54):c.1721C>G (p.Pro574Arg) |
MISSENSE | |
rs1575966808 | Uncertain Significance: Reduced number of teeth | 63,965,958(-) |
C/G NM_016516.3(VPS54):c.501G>C (p.Met167Ile) |
MISSENSE | |
rs193225211 | Benign: not provided | 63,899,588(-) |
G/A NM_016516.3(VPS54):c.2626-7C>T |
INTRON |
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 |
|
|
frontotemporal dementia and/or amyotrophic lateral sclerosis 4 |
|
|
spermatogenic failure 9 |
|
|
frontotemporal dementia and/or amyotrophic lateral sclerosis 2 |
|
|
amyotrophic lateral sclerosis type 22 |
|
|