VPS41 [The Human Chemical-Genetic Interaction Map Project]

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======= VPS41 =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: VPS41
  * **<color #00a2e8>Official Name</color>**: VPS41 subunit of HOPS complex
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=27072|27072]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/P49754|P49754]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=VPS41&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20VPS41|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/605485|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**: N/A
  * **<color #00a2e8>UniProt Summary</color>**:  Plays a role in vesicle-mediated protein trafficking to lysosomal compartments including the endocytic membrane transport and autophagic pathways. Believed to act in part as a core component of the putative HOPS endosomal tethering complex is proposed to be involved in the Rab5-to-Rab7 endosome conversion probably implicating MON1A/B, and via binding SNAREs and SNARE complexes to mediate tethering and docking events during SNARE- mediated membrane fusion. The HOPS complex is proposed to be recruited to Rab7 on the late endosomal membrane and to regulate late endocytic, phagocytic and autophagic traffic towards lysosomes (PubMed:23351085). Involved in homotypic vesicle fusions between late endosomes and in heterotypic fusions between late endosomes and lysosomes implicated in degradation of endocytosed cargo (PubMed:9159129, PubMed:23167963, PubMed:25445562, PubMed:25908847). Required for fusion of autophagosomes with lysosomes (PubMed:25783203). May link the HOPS complex to endosomal Rab7 via its association with RILP and to lysosomal membranes via its association with ARL8B, suggesting that these interactions may bring the compartments to close proximity for fusion (PubMed:25445562, PubMed:25908847). Involved in the direct trans-Golgi network to late endosomes transport of lysosomal membrane proteins independently of HOPS (PubMed:23322049). Involved in sorting to the regulated secretory pathway presumably implicating the AP-3 adaptor complex (By similarity). May play a role in HOPS-independent function in the regulated secretory pathway (PubMed:24210660). {ECO:0000250|UniProtKB:D3ZVH6, ECO:0000269|PubMed:23167963, ECO:0000269|PubMed:23322049, ECO:0000269|PubMed:25445562, ECO:0000269|PubMed:25783203, ECO:0000269|PubMed:25908847, ECO:0000269|PubMed:9159129, ECO:0000305|PubMed:23167963, ECO:0000305|PubMed:23351085, ECO:0000305|PubMed:24210660, ECO:0000305|PubMed:25445562}.

<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'>
|Clathrin|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|vacuole fusion|
|vacuole fusion, non-autophagic|
|late endosome to lysosome transport|
|clathrin complex|
|endosomal vesicle fusion|
|AP-3 adaptor complex|
|regulation of SNARE complex assembly|
|HOPS complex|
|Golgi-associated vesicle|
|regulation of vesicle fusion|
|endosome to lysosome transport|
|protein self-association|
|clathrin-coated vesicle|
|vesicle fusion|
|organelle membrane fusion|
|organelle fusion|
|lysosomal transport|
|late endosome membrane|
|late endosome|
|vacuole organization|
|membrane fusion|
|vacuolar transport|
|microtubule cytoskeleton|
|endosome membrane|
|microtubule binding|
|early endosome|
|autophagy|
|process utilizing autophagic mechanism|
|vesicle organization|
|lysosomal membrane|
|regulation of protein complex assembly|
|regulation of vesicle-mediated transport|
|regulated exocytosis|
|exocytosis|
|membrane organization|
|regulation of cellular component biogenesis|
|Golgi apparatus|
|intracellular protein transport|
|secretion by cell|
|export from cell|
|identical protein binding|
|secretion|
|regulation of organelle organization|
|protein transport|
|intracellular transport|
|peptide transport|
|amide transport|
|cellular protein localization|
|cellular macromolecule localization|
|establishment of protein localization|
|cellular catabolic process|
|establishment of localization in cell|
|nitrogen compound transport|
|regulation of 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:exp389|PF-06409577 20μM R07 exp389]]|-1.83|
|[[:results:exp222|Betulinic acid 10 to 15μM on day4 R05 exp222]]|-1.8|
|[[:results:exp412|THZ531 0.11 to 0.125 to 0.35μM on day4 then day6 R07 exp412]]|-1.8|
|[[:results:exp187|proTAME 5μM R04 exp187]]|-1.78|
|[[:results:exp37|Wortmannin 0.5μM R00 exp37]]|-1.73|
|[[:results:exp435|JQ1 0.8μM R08 exp435]]|1.72|
|[[:results:exp515|PU-H71 1μM R08 exp515]]|1.74|
|[[:results:exp36|TRAIL 50ng/ml R00 exp36]]|1.78|
|[[:results:exp513|ONC212 0.15μM R08 exp513]]|1.9|
|[[:results:exp499|LY2090314 0.003μM R08 exp499]]|2|
|[[:results:exp500|LY2090314 0.003μM R08 exp500 no dilution day6]]|2.16|
|[[:results:exp24|Nocodazole 0.2μM R00 exp24]]|2.16|
|[[:results:exp94|Nocodazole 0.1μM R03 exp94]]|2.29|
|[[:results:exp208|Vinblastine 0.015μM R05 exp208]]|2.32|
|[[:results:exp111|R-DABN 8μM R03 exp111]]|2.33|
|[[:results:exp33|Rotenone 2μM R00 exp33]]|2.92|
|[[:results:exp244|SB743921 0.001μM R05 exp244]]|3.05|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
^Gene^Correlation^
|[[:human genes:l:lamtor4|LAMTOR4]]|0.568|
|[[:human genes:w:wdr24|WDR24]]|0.527|
|[[:human genes:f:flcn|FLCN]]|0.494|
|[[:human genes:l:lamtor3|LAMTOR3]]|0.487|
|[[:human genes:l:lamtor5|LAMTOR5]]|0.484|
|[[:human genes:d:dohh|DOHH]]|0.478|
|[[:human genes:p:ppa2|PPA2]]|0.471|
|[[:human genes:h:hgc6.3|HGC6.3]]|0.468|
|[[:human genes:l:lamtor2|LAMTOR2]]|0.458|
|[[:human genes:f:fnip1|FNIP1]]|0.454|
|[[:human genes:t:tefm|TEFM]]|0.448|
|[[:human genes:t:tbc1d5|TBC1D5]]|0.44|
|[[:human genes:m:mtmr6|MTMR6]]|0.426|
|[[:human genes:r:rptor|RPTOR]]|0.425|
|[[:human genes:m:mios|MIOS]]|0.425|
|[[:human genes:t:trmt10a|TRMT10A]]|0.422|
|[[:human genes:k:kdsr|KDSR]]|0.422|
|[[:human genes:t:thg1l|THG1L]]|0.419|
|[[:human genes:t:trnt1|TRNT1]]|0.417|
|[[:human genes:e:exoc4|EXOC4]]|0.416|
|[[:human genes:u:uqcr10|UQCR10]]|0.415|
|[[:human genes:a:alg13|ALG13]]|0.413|
|[[:human genes:v:vps35|VPS35]]|0.411|
|[[:human genes:t:tbp|TBP]]|0.411|
|[[:human genes:r:rnmt|RNMT]]|0.408|
|[[:human genes:u:urm1|URM1]]|0.408|
|[[:human genes:w:wdr59|WDR59]]|0.407|
|[[:human genes:v:vps26a|VPS26A]]|0.407|
|[[:human genes:g:gtf2a2|GTF2A2]]|0.405|
|[[:human genes:l:lipa|LIPA]]|0.401|
|[[:human genes:t:tufm|TUFM]]|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: 528/739
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|1/1|
|909776.0|1/1|
|bile duct|22/28|
|blood|24/28|
|bone|21/26|
|breast|22/33|
|central nervous system|24/56|
|cervix|3/4|
|colorectal|11/17|
|esophagus|6/13|
|fibroblast|1/1|
|gastric|11/16|
|kidney|16/21|
|liver|15/20|
|lung|57/75|
|lymphocyte|16/16|
|ovary|20/26|
|pancreas|19/24|
|peripheral nervous system|13/16|
|plasma cell|14/15|
|prostate|1/1|
|skin|10/24|
|soft tissue|9/9|
|thyroid|2/2|
|upper aerodigestive|16/22|
|urinary tract|22/29|
|uterus|5/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 6030
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 5.83 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='VPS41 Expression in NALM6 Cells: 5.83'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>