Details for: VPS54

Gene ID: 51542

Symbol: VPS54

Ensembl ID: ENSG00000143952

Description: VPS54 subunit of GARP complex

Associated with

Cells (max top 100)

(Cell Significance Index and respective Thresholds are uniquely calculated using our advanced thresholding algorithms to reveal cell-specific gene markers)

  • Cell Name: polychromatophilic erythroblast (CL0000550)
    Fold Change: 314.6995
    Cell Significance Index: -48.9500
  • Cell Name: hematopoietic oligopotent progenitor cell (CL0002032)
    Fold Change: 194.0520
    Cell Significance Index: -49.2200
  • Cell Name: mucosal type mast cell (CL0000485)
    Fold Change: 98.9029
    Cell Significance Index: -40.1800
  • Cell Name: ciliated cell of the bronchus (CL0002332)
    Fold Change: 42.1265
    Cell Significance Index: -40.2200
  • Cell Name: orthochromatic erythroblast (CL0000552)
    Fold Change: 40.0420
    Cell Significance Index: -49.3700
  • Cell Name: CD8-positive, alpha-beta regulatory T cell (CL0000795)
    Fold Change: 12.9515
    Cell Significance Index: -39.7800
  • Cell Name: stromal cell of bone marrow (CL0010001)
    Fold Change: 12.5467
    Cell Significance Index: -49.5100
  • Cell Name: epidermal Langerhans cell (CL0002457)
    Fold Change: 11.3589
    Cell Significance Index: -24.8600
  • Cell Name: skeletal muscle fiber (CL0008002)
    Fold Change: 3.4492
    Cell Significance Index: 88.6600
  • Cell Name: neoplastic cell (CL0001063)
    Fold Change: 3.1810
    Cell Significance Index: 631.2800
  • Cell Name: retinal progenitor cell (CL0002672)
    Fold Change: 2.1647
    Cell Significance Index: 121.4700
  • Cell Name: preadipocyte (CL0002334)
    Fold Change: 2.1566
    Cell Significance Index: 42.0900
  • Cell Name: L2/3-6 intratelencephalic projecting glutamatergic neuron (CL4023040)
    Fold Change: 1.9643
    Cell Significance Index: 394.0300
  • Cell Name: cardiac muscle myoblast (CL0000513)
    Fold Change: 1.9056
    Cell Significance Index: 146.2400
  • Cell Name: microfold cell of epithelium of small intestine (CL1000353)
    Fold Change: 1.6880
    Cell Significance Index: 116.7400
  • Cell Name: epithelial cell of small intestine (CL0002254)
    Fold Change: 1.5374
    Cell Significance Index: 250.0400
  • Cell Name: obsolete caudal ganglionic eminence derived GABAergic cortical interneuron (CL4023070)
    Fold Change: 1.3879
    Cell Significance Index: 497.8000
  • Cell Name: leptomeningeal cell (CL0000708)
    Fold Change: 1.1546
    Cell Significance Index: 24.6800
  • Cell Name: basal epithelial cell of tracheobronchial tree (CL0002329)
    Fold Change: 1.1236
    Cell Significance Index: 31.4000
  • Cell Name: enteroendocrine cell of small intestine (CL0009006)
    Fold Change: 1.0285
    Cell Significance Index: 25.7100
  • Cell Name: GABAergic interneuron (CL0011005)
    Fold Change: 1.0174
    Cell Significance Index: 703.6900
  • Cell Name: forebrain neuroblast (CL1000042)
    Fold Change: 0.9308
    Cell Significance Index: 57.2100
  • Cell Name: intestinal crypt stem cell of colon (CL0009043)
    Fold Change: 0.9078
    Cell Significance Index: 98.7500
  • Cell Name: indirect pathway medium spiny neuron (CL4023029)
    Fold Change: 0.8966
    Cell Significance Index: 39.6600
  • Cell Name: hippocampal granule cell (CL0001033)
    Fold Change: 0.8627
    Cell Significance Index: 58.0100
  • Cell Name: direct pathway medium spiny neuron (CL4023026)
    Fold Change: 0.8400
    Cell Significance Index: 31.8100
  • Cell Name: cardiac endothelial cell (CL0010008)
    Fold Change: 0.6838
    Cell Significance Index: 9.8400
  • Cell Name: tuft cell of colon (CL0009041)
    Fold Change: 0.4819
    Cell Significance Index: 435.1400
  • Cell Name: gut absorptive cell (CL0000677)
    Fold Change: 0.4625
    Cell Significance Index: 27.7700
  • Cell Name: cortical interneuron (CL0008031)
    Fold Change: 0.4612
    Cell Significance Index: 11.0600
  • Cell Name: paneth cell of epithelium of small intestine (CL1000343)
    Fold Change: 0.4487
    Cell Significance Index: 9.7200
  • Cell Name: acinar cell of salivary gland (CL0002623)
    Fold Change: 0.4230
    Cell Significance Index: 19.7200
  • Cell Name: enterocyte of epithelium of large intestine (CL0002071)
    Fold Change: 0.2923
    Cell Significance Index: 13.2500
  • Cell Name: ciliary muscle cell (CL1000443)
    Fold Change: 0.2611
    Cell Significance Index: 118.5200
  • Cell Name: pigmented epithelial cell (CL0000529)
    Fold Change: 0.2570
    Cell Significance Index: 483.8900
  • Cell Name: cortical cell of adrenal gland (CL0002097)
    Fold Change: 0.2493
    Cell Significance Index: 6.6800
  • Cell Name: intermediate cell of urothelium (CL4030055)
    Fold Change: 0.2238
    Cell Significance Index: 40.3500
  • Cell Name: basal cell of urothelium (CL1000486)
    Fold Change: 0.2158
    Cell Significance Index: 26.5400
  • Cell Name: colon goblet cell (CL0009039)
    Fold Change: 0.2124
    Cell Significance Index: 21.0100
  • Cell Name: centrilobular region hepatocyte (CL0019029)
    Fold Change: 0.1828
    Cell Significance Index: 3.0800
  • Cell Name: lens epithelial cell (CL0002224)
    Fold Change: 0.1613
    Cell Significance Index: 248.2600
  • Cell Name: non-pigmented ciliary epithelial cell (CL0002304)
    Fold Change: 0.1592
    Cell Significance Index: 101.1300
  • Cell Name: anterior lens cell (CL0002223)
    Fold Change: 0.1459
    Cell Significance Index: 269.0500
  • Cell Name: secondary lens fiber (CL0002225)
    Fold Change: 0.1406
    Cell Significance Index: 191.2100
  • Cell Name: enteroendocrine cell of colon (CL0009042)
    Fold Change: 0.1205
    Cell Significance Index: 22.9300
  • Cell Name: cell in vitro (CL0001034)
    Fold Change: 0.1016
    Cell Significance Index: 55.5000
  • Cell Name: cerebellar granule cell (CL0001031)
    Fold Change: 0.1010
    Cell Significance Index: 1.7300
  • Cell Name: enterocyte of epithelium of small intestine (CL1000334)
    Fold Change: 0.0939
    Cell Significance Index: 2.7100
  • Cell Name: fibroblast of cardiac tissue (CL0002548)
    Fold Change: 0.0655
    Cell Significance Index: 0.9400
  • Cell Name: hippocampal pyramidal neuron (CL1001571)
    Fold Change: 0.0648
    Cell Significance Index: 1.8500
  • Cell Name: hair follicular keratinocyte (CL2000092)
    Fold Change: 0.0461
    Cell Significance Index: 20.3800
  • Cell Name: conjunctival epithelial cell (CL1000432)
    Fold Change: 0.0388
    Cell Significance Index: 0.5300
  • Cell Name: small intestine goblet cell (CL1000495)
    Fold Change: 0.0344
    Cell Significance Index: 1.2100
  • Cell Name: pancreatic acinar cell (CL0002064)
    Fold Change: 0.0012
    Cell Significance Index: 0.2100
  • Cell Name: stromal cell of ovary (CL0002132)
    Fold Change: -0.0170
    Cell Significance Index: -2.3400
  • Cell Name: pigmented ciliary epithelial cell (CL0002303)
    Fold Change: -0.0431
    Cell Significance Index: -6.2600
  • Cell Name: pancreatic A cell (CL0000171)
    Fold Change: -0.0446
    Cell Significance Index: -33.0500
  • Cell Name: kidney loop of Henle cortical thick ascending limb epithelial cell (CL1001109)
    Fold Change: -0.0470
    Cell Significance Index: -34.4500
  • Cell Name: luminal adaptive secretory precursor cell of mammary gland (CL4033057)
    Fold Change: -0.0585
    Cell Significance Index: -2.7500
  • Cell Name: pulmonary alveolar epithelial cell (CL0000322)
    Fold Change: -0.0589
    Cell Significance Index: -44.5500
  • Cell Name: type B pancreatic cell (CL0000169)
    Fold Change: -0.0780
    Cell Significance Index: -44.0100
  • Cell Name: pancreatic PP cell (CL0002275)
    Fold Change: -0.0875
    Cell Significance Index: -54.6600
  • Cell Name: type I muscle cell (CL0002211)
    Fold Change: -0.1021
    Cell Significance Index: -2.4900
  • Cell Name: dopaminergic neuron (CL0000700)
    Fold Change: -0.1506
    Cell Significance Index: -43.3300
  • Cell Name: odontoblast (CL0000060)
    Fold Change: -0.1770
    Cell Significance Index: -22.6900
  • Cell Name: epithelial cell of stomach (CL0002178)
    Fold Change: -0.1997
    Cell Significance Index: -23.2700
  • Cell Name: placental villous trophoblast (CL2000060)
    Fold Change: -0.2142
    Cell Significance Index: -5.7200
  • Cell Name: smooth muscle cell of sphincter of pupil (CL0002243)
    Fold Change: -0.2148
    Cell Significance Index: -22.3700
  • Cell Name: endothelial cell of placenta (CL0009092)
    Fold Change: -0.2383
    Cell Significance Index: -1.4400
  • Cell Name: pancreatic D cell (CL0000173)
    Fold Change: -0.2427
    Cell Significance Index: -51.1200
  • Cell Name: pancreatic ductal cell (CL0002079)
    Fold Change: -0.2542
    Cell Significance Index: -29.1300
  • Cell Name: lactocyte (CL0002325)
    Fold Change: -0.2901
    Cell Significance Index: -37.4800
  • Cell Name: abnormal cell (CL0001061)
    Fold Change: -0.2957
    Cell Significance Index: -30.2100
  • Cell Name: bladder urothelial cell (CL1001428)
    Fold Change: -0.3054
    Cell Significance Index: -15.8700
  • Cell Name: intestinal crypt stem cell of small intestine (CL0009017)
    Fold Change: -0.3205
    Cell Significance Index: -6.8200
  • Cell Name: tonsil germinal center B cell (CL2000006)
    Fold Change: -0.3492
    Cell Significance Index: -41.1900
  • Cell Name: cardiac muscle cell (CL0000746)
    Fold Change: -0.3685
    Cell Significance Index: -5.4400
  • Cell Name: sebum secreting cell (CL0000317)
    Fold Change: -0.4457
    Cell Significance Index: -31.5200
  • Cell Name: eye photoreceptor cell (CL0000287)
    Fold Change: -0.4461
    Cell Significance Index: -28.1200
  • Cell Name: lung endothelial cell (CL1001567)
    Fold Change: -0.4533
    Cell Significance Index: -23.6100
  • Cell Name: progenitor cell of mammary luminal epithelium (CL0009116)
    Fold Change: -0.5152
    Cell Significance Index: -38.4000
  • Cell Name: intestinal tuft cell (CL0019032)
    Fold Change: -0.5237
    Cell Significance Index: -32.1100
  • Cell Name: kidney loop of Henle descending limb epithelial cell (CL1001021)
    Fold Change: -0.5387
    Cell Significance Index: -42.6600
  • Cell Name: early pro-B cell (CL0002046)
    Fold Change: -0.5436
    Cell Significance Index: -35.0700
  • Cell Name: periportal region hepatocyte (CL0019026)
    Fold Change: -0.5860
    Cell Significance Index: -8.6500
  • Cell Name: Purkinje cell (CL0000121)
    Fold Change: -0.6549
    Cell Significance Index: -14.3400
  • Cell Name: OFF midget ganglion cell (CL4033047)
    Fold Change: -0.6817
    Cell Significance Index: -8.5000
  • Cell Name: pvalb GABAergic cortical interneuron (CL4023018)
    Fold Change: -0.6926
    Cell Significance Index: -14.7000
  • Cell Name: corticothalamic-projecting glutamatergic cortical neuron (CL4023013)
    Fold Change: -0.7514
    Cell Significance Index: -23.9300
  • Cell Name: skeletal muscle fibroblast (CL0011027)
    Fold Change: -0.7571
    Cell Significance Index: -5.1300
  • Cell Name: L6b glutamatergic cortical neuron (CL4023038)
    Fold Change: -0.7670
    Cell Significance Index: -25.1100
  • Cell Name: glycinergic neuron (CL1001509)
    Fold Change: -0.7733
    Cell Significance Index: -40.6000
  • Cell Name: adipocyte of breast (CL0002617)
    Fold Change: -0.7751
    Cell Significance Index: -9.7600
  • Cell Name: basal cell of prostate epithelium (CL0002341)
    Fold Change: -0.7978
    Cell Significance Index: -21.7200
  • Cell Name: sst GABAergic cortical interneuron (CL4023017)
    Fold Change: -0.8259
    Cell Significance Index: -16.3300
  • Cell Name: transit amplifying cell of colon (CL0009011)
    Fold Change: -0.8564
    Cell Significance Index: -27.4300
  • Cell Name: BEST4+ enteroycte (CL4030026)
    Fold Change: -0.8892
    Cell Significance Index: -13.4000
  • Cell Name: VIP GABAergic cortical interneuron (CL4023016)
    Fold Change: -0.9006
    Cell Significance Index: -18.0800
  • Cell Name: ON midget ganglion cell (CL4033046)
    Fold Change: -0.9215
    Cell Significance Index: -11.6300
  • Cell Name: L5 extratelencephalic projecting glutamatergic cortical neuron (CL4023041)
    Fold Change: -1.0276
    Cell Significance Index: -36.0000

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Other Information

**Key Characteristics:** The VPS54 gene is a member of the VPS (Vacuolar Protein Sorting) family of genes, which play a vital role in the sorting and transport of proteins within the cell. The VPS54 subunit is specifically associated with the GARP complex, which has been implicated in the regulation of apoptosis and cellular differentiation. The gene is also involved in the regulation of intracellular calcium ion homeostasis, a critical process that maintains cellular function and viability. **Pathways and Functions:** The VPS54 gene is involved in various cellular pathways, including: 1. **Apoptotic DNA fragmentation**: The VPS54 subunit is involved in the regulation of apoptosis, a process of programmed cell death that plays a crucial role in maintaining tissue homeostasis. 2. **Astrocyte differentiation**: The gene is also involved in the differentiation of astrocytes, a type of glial cell that plays a critical role in maintaining the health and function of the central nervous system. 3. **Intracellular calcium ion homeostasis**: The VPS54 subunit is involved in the regulation of intracellular calcium ion homeostasis, a critical process that maintains cellular function and viability. 4. **Golgi apparatus and retrograde transport**: The gene is involved in the regulation of Golgi apparatus function and retrograde transport, a process that is critical for the sorting and transport of proteins within the cell. **Clinical Significance:** The VPS54 gene has significant clinical implications, particularly in the context of: 1. **Neurological disorders**: The gene's involvement in astrocyte differentiation and intracellular calcium ion homeostasis makes it a potential target for the treatment of neurological disorders, such as Alzheimer's disease and Parkinson's disease. 2. **Cancer**: The gene's role in apoptosis and cellular differentiation makes it a potential target for the treatment of cancer, particularly in the context of cancer therapy-induced apoptosis. 3. **Musculoskeletal disorders**: The gene's involvement in muscle fiber development and function makes it a potential target for the treatment of musculoskeletal disorders, such as muscular dystrophy. In conclusion, the VPS54 gene plays a critical role in maintaining cellular homeostasis and has significant clinical implications in the context of neurological disorders, cancer, and musculoskeletal disorders. Further research is needed to fully understand the functional significance of the VPS54 gene and its potential therapeutic applications.

Genular Protein ID: 1460784805

Symbol: VPS54_HUMAN

Name: Vacuolar protein sorting-associated protein 54

UniProtKB Accession Codes:

Q9P1Q0 Q5VIR5 Q86YF7 Q8N6G3 Q9NPV0 Q9NT07 Q9NUJ0

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 2 CORUM 1 CTD 1 ChiTaRS 1 ComplexPortal 1 DIP 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 8 Ensembl 3 ExpressionAtlas 1 GO 51 Gene3D 2 GeneCards 1 GeneTree 1 GenomeRNAi 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 3 KEGG 1 MANE-Select 1 MIM 1 MINT 1 MassIVE 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 OrthoDB 1 PANTHER 2 PIR 1 PRO 1 PathwayCommons 1 PaxDb 1 PeptideAtlas 1 Pfam 2 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 5 Pumba 1 RNAct 1 Reactome 1 RefSeq 2 SMR 1 STRING 1 SignaLink 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 jPOST 1 neXtProt 1

Citations:

PubMed ID: 15878329

Title: Characterization of the human GARP (Golgi associated retrograde protein) complex.

PubMed ID: 15878329

DOI: 10.1016/j.yexcr.2005.01.022

PubMed ID: 17974005

Title: The full-ORF clone resource of the German cDNA consortium.

PubMed ID: 17974005

DOI: 10.1186/1471-2164-8-399

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 14702039

Title: Complete sequencing and characterization of 21,243 full-length human cDNAs.

PubMed ID: 14702039

DOI: 10.1038/ng1285

PubMed ID: 18367545

Title: Requirement of the human GARP complex for mannose 6-phosphate-receptor-dependent sorting of cathepsin D to lysosomes.

PubMed ID: 18367545

DOI: 10.1091/mbc.e07-11-1189

PubMed ID: 20685960

Title: Ang2/fat-free is a conserved subunit of the Golgi-associated retrograde protein complex.

PubMed ID: 20685960

DOI: 10.1091/mbc.e10-05-0392

PubMed ID: 23186163

Title: Toward a comprehensive characterization of a human cancer cell phosphoproteome.

PubMed ID: 23186163

DOI: 10.1021/pr300630k

PubMed ID: 25799061

Title: EARP is a multisubunit tethering complex involved in endocytic recycling.

PubMed ID: 25799061

DOI: 10.1038/ncb3129

PubMed ID: 27440922

Title: TSSC1 is novel component of the endosomal retrieval machinery.

PubMed ID: 27440922

DOI: 10.1091/mbc.e16-04-0209

PubMed ID: 31721635

Title: EIPR1 controls dense-core vesicle cargo retention and EARP complex localization in insulin-secreting cells.

PubMed ID: 31721635

DOI: 10.1091/mbc.e18-07-0469

Sequence Information:

  • Length: 977
  • Mass: 110589
  • Checksum: 3290160E3460C836
  • Sequence:
    • MASSHSSSPV PQGSSSDVFF KIEVDPSKHI RPVPSLPDVC PKEPTGDSHS LYVAPSLVTD 
QHRWTVYHSK VNLPAALNDP RLAKRESDFF TKTWGLDFVD TEVIPSFYLP QISKEHFTVY 
QQEISQREKI HERCKNICPP KDTFERTLLH THDKSRTDLE QVPKIFMKPD FALDDSLTFN 
SVLPWSHFNT AGGKGNRDAA SSKLLQEKLS HYLDIVEVNI AHQISLRSEA FFHAMTSQHE 
LQDYLRKTSQ AVKMLRDKIA QIDKVMCEGS LHILRLALTR NNCVKVYNKL KLMATVHQTQ 
PTVQVLLSTS EFVGALDLIA TTQEVLQQEL QGIHSFRHLG SQLCELEKLI DKMMIAEFST 
YSHSDLNRPL EDDCQVLEEE RLISLVFGLL KQRKLNFLEI YGEKMVITAK NIIKQCVINK 
VSQTEEIDTD VVVKLADQMR MLNFPQWFDL LKDIFSKFTI FLQRVKATLN IIHSVVLSVL 
DKNQRTRELE EISQQKNAAK DNSLDTEVAY LIHEGMFISD AFGEGELTPI AVDTTSQRNA 
SPNSEPCSSD SVSEPECTTD SSSSKEHTSS SAIPGGVDIM VSEDMKLTDS ELGKLANNIQ 
ELLYSASDIC HDRAVKFLMS RAKDGFLEKL NSMEFITLSR LMETFILDTE QICGRKSTSL 
LGALQSQAIK FVNRFHEERK TKLSLLLDNE RWKQADVPAE FQDLVDSLSD GKIALPEKKS 
GATEERKPAE VLIVEGQQYA VVGTVLLLIR IILEYCQCVD NIPSVTTDML TRLSDLLKYF 
NSRSCQLVLG AGALQVVGLK TITTKNLALS SRCLQLIVHY IPVIRAHFEA RLPPKQYSML 
RHFDHITKDY HDHIAEISAK LVAIMDSLFD KLLSKYEVKA PVPSACFRNI CKQMTKMHEA 
IFDLLPEEQT QMLFLRINAS YKLHLKKQLS HLNVINDGGP QNGLVTADVA FYTGNLQALK 
GLKDLDLNMA EIWEQKR

Database document:

This is a preview of the gene's schema. Only a few entries are kept for 'singleCellExpressions,' 'mRNAExpressions,' and other large data arrays for visualization purposes. You can zoom in with the mouse wheel for a closer view, and the text will adjust automatically if necessary. For the full schema, download it here.