VPS54 [The Human Chemical-Genetic Interaction Map Project]

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======= VPS54 =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: VPS54
  * **<color #00a2e8>Official Name</color>**: VPS54 subunit of GARP complex
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=51542|51542]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/Q9P1Q0|Q9P1Q0]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=VPS54&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20VPS54|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/614633|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  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]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Acts as component of the GARP complex that is involved in retrograde transport from early and late endosomes to the trans-Golgi network (TGN). The GARP complex is required for the maintenance of the cycling of mannose 6-phosphate receptors between the TGN and endosomes, this cycling is necessary for proper lysosomal sorting of acid hydrolases such as CTSD (PubMed:18367545). Within the GARP complex, required to tether the complex to the TGN. Not involved in endocytic recycling (PubMed:25799061). {ECO:0000269|PubMed:18367545, ECO:0000269|PubMed:25799061}.

<button type='primary' size='sm' modal='Pfam_Domains'>Pfam Domains</button>
<button type='primary' size='sm' modal='GO_terms'>GO Terms</button>


<modal id='Pfam_Domains' size='lg' title='Pfam Domains'>
|Vps54|
|DUF2450|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|GARP complex|
|neurofilament cytoskeleton organization|
|Golgi to vacuole transport|
|homeostasis of number of cells within a tissue|
|multicellular organismal movement|
|musculoskeletal movement|
|intermediate filament cytoskeleton organization|
|intermediate filament-based process|
|syntaxin binding|
|trans-Golgi network membrane|
|retrograde transport, endosome to Golgi|
|post-Golgi vesicle-mediated transport|
|lysosomal transport|
|vacuolar transport|
|cytosolic transport|
|trans-Golgi network|
|tissue homeostasis|
|homeostasis of number of cells|
|endosomal transport|
|multicellular organismal homeostasis|
|anatomical structure homeostasis|
|Golgi vesicle transport|
|regulation of growth|
|perinuclear region of cytoplasm|
|Golgi apparatus|
|cytoskeleton organization|
|protein transport|
|intracellular transport|
|peptide transport|
|amide transport|
|establishment of protein localization|
|homeostatic process|
|establishment of localization in cell|
|nitrogen compound transport|
|vesicle-mediated transport|
</modal>
\\

 === CRISPR Data ===
<button type='primary' size='small' modal='Compound_Hit'>Compound Hit</button>
<button type='primary' size='small' modal='Most_Correlated_Genes'>Most Correlated Genes in Chemogenomics</button>
<button type='primary' size='small' modal='Essential_Avana'>Tissues where Essential in the Avana Dataset (DepMap 20Q1)</button>

<modal id='Compound_Hit' size='lg' title='Compound Hit'>
^Screen^Score^
|[[:results:exp89|Vemurafenib 6.6μM R02 exp89]]|-2.49|
|[[:results:exp527|Tanespimycin 14μM R08 exp527]]|-2.39|
|[[:results:exp487|Hinokiflavone 12μM R08 exp487]]|-2.38|
|[[:results:exp515|PU-H71 1μM R08 exp515]]|-2.18|
|[[:results:exp269|Bisphenol A 100μM R06 exp269]]|-2.14|
|[[:results:exp447|Amiloride 100μM R08 exp447]]|-2.13|
|[[:results:exp382|Palbociclib 1μM R07 exp382]]|-2.1|
|[[:results:exp469|CFI-400945 25μM R08 exp469]]|-1.95|
|[[:results:exp454|Bafilomycin-A1 0.009μM R08 exp454]]|-1.93|
|[[:results:exp7|Bortezomib 0.05μM R00 exp7]]|-1.91|
|[[:results:exp79|Q15 2.7μM R02 exp79]]|-1.91|
|[[:results:exp26|Oligomycin-A 20μM R00 exp26]]|-1.9|
|[[:results:exp434|Vemurafenib 6.6μM R08 exp434]]|-1.9|
|[[:results:exp20|Etoposide 10μM R00 exp20]]|-1.82|
|[[:results:exp22|MLN-4924 2μM R00 exp22]]|-1.82|
|[[:results:exp126|GSK461364A 0.1μM R03 exp126]]|-1.74|
|[[:results:exp350|Deferoxamine 11μM R07 exp350]]|-1.71|
|[[:results:exp16|DABN 2μM R00 exp16]]|1.86|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
^Gene^Correlation^
|[[:human genes:c:copz1|COPZ1]]|0.563|
|[[:human genes:c:copg1|COPG1]]|0.547|
|[[:human genes:o:ogfr|OGFR]]|0.513|
|[[:human genes:a:arcn1|ARCN1]]|0.505|
|[[:human genes:z:znf106|ZNF106]]|0.501|
|[[:human genes:p:psmb4|PSMB4]]|0.496|
|[[:human genes:t:tfip11|TFIP11]]|0.493|
|[[:human genes:c:copa|COPA]]|0.492|
|[[:human genes:p:polr2j3|POLR2J3]]|0.491|
|[[:human genes:v:vps52|VPS52]]|0.49|
|[[:human genes:s:supt6h|SUPT6H]]|0.49|
|[[:human genes:t:tssc1|TSSC1]]|0.483|
|[[:human genes:c:copb1|COPB1]]|0.482|
|[[:human genes:m:myb|MYB]]|0.477|
|[[:human genes:t:twistnb|TWISTNB]]|0.477|
|[[:human genes:s:stil|STIL]]|0.471|
|[[:human genes:v:vasn|VASN]]|0.468|
|[[:human genes:c:chd4|CHD4]]|0.468|
|[[:human genes:a:akirin2|AKIRIN2]]|0.467|
|[[:human genes:a:atp6v1c1|ATP6V1C1]]|0.464|
|[[:human genes:c:copb2|COPB2]]|0.463|
|[[:human genes:t:tbc1d3g|TBC1D3G]]|0.46|
|[[:human genes:d:dtl|DTL]]|0.459|
|[[:human genes:p:polr2d|POLR2D]]|0.459|
|[[:human genes:t:trappc8|TRAPPC8]]|0.459|
|[[:human genes:c:cbwd3|CBWD3]]|0.459|
|[[:human genes:s:supt5h|SUPT5H]]|0.452|
|[[:human genes:s:sys1|SYS1]]|0.45|
|[[:human genes:p:polr1a|POLR1A]]|0.449|
|[[:human genes:g:gprin2|GPRIN2]]|0.448|
|[[:human genes:s:smg1|SMG1]]|0.447|
|[[:human genes:n:narfl|NARFL]]|0.447|
|[[:human genes:t:taf1|TAF1]]|0.447|
|[[:human genes:t:trappc11|TRAPPC11]]|0.446|
|[[:human genes:a:aamp|AAMP]]|0.444|
|[[:human genes:c:cbwd5|CBWD5]]|0.441|
|[[:human genes:r:rbm39|RBM39]]|0.441|
|[[:human genes:g:golga6b|GOLGA6B]]|0.44|
|[[:human genes:s:sec13|SEC13]]|0.44|
|[[:human genes:y:ythdc1|YTHDC1]]|0.439|
|[[:human genes:t:ticrr|TICRR]]|0.438|
|[[:human genes:a:atp6v1a|ATP6V1A]]|0.438|
|[[:human genes:t:trappc2l|TRAPPC2L]]|0.438|
|[[:human genes:o:orc1|ORC1]]|0.437|
|[[:human genes:t:tbc1d3h|TBC1D3H]]|0.437|
|[[:human genes:t:topbp1|TOPBP1]]|0.437|
|[[:human genes:n:napa|NAPA]]|0.436|
|[[:human genes:g:gosr2|GOSR2]]|0.435|
|[[:human genes:r:ranbp2|RANBP2]]|0.433|
|[[:human genes:k:kctd17|KCTD17]]|0.433|
|[[:human genes:a:atxn1|ATXN1]]|0.432|
|[[:human genes:c:cwc15|CWC15]]|0.432|
|[[:human genes:r:riok2|RIOK2]]|0.432|
|[[:human genes:a:atp1a3|ATP1A3]]|0.431|
|[[:human genes:n:nol12|NOL12]]|0.43|
|[[:human genes:a:aatf|AATF]]|0.43|
|[[:human genes:t:tceb3cl2|TCEB3CL2]]|0.429|
|[[:human genes:c:cbwd6|CBWD6]]|0.427|
|[[:human genes:r:rint1|RINT1]]|0.426|
|[[:human genes:z:znf655|ZNF655]]|0.426|
|[[:human genes:f:fam160a1|FAM160A1]]|0.426|
|[[:human genes:n:npipb5|NPIPB5]]|0.425|
|[[:human genes:d:disp2|DISP2]]|0.425|
|[[:human genes:s:slc4a1|SLC4A1]]|0.423|
|[[:human genes:p:psma6|PSMA6]]|0.423|
|[[:human genes:k:kif3c|KIF3C]]|0.422|
|[[:human genes:n:nufip2|NUFIP2]]|0.421|
|[[:human genes:s:sh3bp1|SH3BP1]]|0.42|
|[[:human genes:t:tbc1d3f|TBC1D3F]]|0.419|
|[[:human genes:i:ints1|INTS1]]|0.417|
|[[:human genes:t:tceb3cl|TCEB3CL]]|0.417|
|[[:human genes:t:tp53tg3b|TP53TG3B]]|0.417|
|[[:human genes:t:tp53tg3|TP53TG3]]|0.416|
|[[:human genes:h:hist1h2be|HIST1H2BE]]|0.415|
|[[:human genes:t:tp53tg3c|TP53TG3C]]|0.415|
|[[:human genes:p:pi4kb|PI4KB]]|0.415|
|[[:human genes:u:ubap1|UBAP1]]|0.414|
|[[:human genes:t:tbc1d3c|TBC1D3C]]|0.413|
|[[:human genes:o:osbp|OSBP]]|0.412|
|[[:human genes:i:ints6|INTS6]]|0.412|
|[[:human genes:a:acsf2|ACSF2]]|0.412|
|[[:human genes:s:samd1|SAMD1]]|0.411|
|[[:human genes:s:snrpa1|SNRPA1]]|0.411|
|[[:human genes:n:nbpf10|NBPF10]]|0.41|
|[[:human genes:p:pan3|PAN3]]|0.41|
|[[:human genes:d:ddtl|DDTL]]|0.41|
|[[:human genes:c:ctage9|CTAGE9]]|0.409|
|[[:human genes:u:utp3|UTP3]]|0.409|
|[[:human genes:r:rad51|RAD51]]|0.409|
|[[:human genes:s:ssh2|SSH2]]|0.408|
|[[:human genes:p:psmb1|PSMB1]]|0.408|
|[[:human genes:c:cog4|COG4]]|0.408|
|[[:human genes:o:orc6|ORC6]]|0.408|
|[[:human genes:t:tceb3c|TCEB3C]]|0.407|
|[[:human genes:c:cdc45|CDC45]]|0.404|
|[[:human genes:r:rps19|RPS19]]|0.404|
|[[:human genes:a:ankle1|ANKLE1]]|0.404|
|[[:human genes:p:prim1|PRIM1]]|0.404|
|[[:human genes:n:nipbl|NIPBL]]|0.404|
|[[:human genes:a:atp6v0a2|ATP6V0A2]]|0.403|
|[[:human genes:d:dnm2|DNM2]]|0.402|
|[[:human genes:p:polr2f|POLR2F]]|0.401|
|[[:human genes:a:atp6v1b2|ATP6V1B2]]|0.4|
</modal>

<modal id='Essential_Avana' size='lg' title='Tissues where Essential in the Avana Dataset (DepMap 20Q1)'>
Global Fraction of Cell Lines Where Essential: 42/739
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|1/1|
|bile duct|2/28|
|blood|2/28|
|bone|0/26|
|breast|0/33|
|central nervous system|4/56|
|cervix|0/4|
|colorectal|2/17|
|esophagus|1/13|
|fibroblast|1/1|
|gastric|0/16|
|kidney|1/21|
|liver|2/20|
|lung|7/75|
|lymphocyte|2/16|
|ovary|0/26|
|pancreas|0/24|
|peripheral nervous system|3/16|
|plasma cell|4/15|
|prostate|0/1|
|skin|0/24|
|soft tissue|0/9|
|thyroid|0/2|
|upper aerodigestive|5/22|
|urinary tract|0/29|
|uterus|0/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 990
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 5.14 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='VPS54 Expression in NALM6 Cells: 5.14'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>