Atlas of Genetics and Cytogenetics in Oncology and Haematology

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LPCAT1 (lysophosphatidylcholine acyltransferase 1)

Identity

Alias_namesAYTL2
acyltransferase like 2
Alias_symbol (synonym)FLJ12443
AGPAT9
AGPAT10
Other aliasLPCAT-1
PFAAP3
lpcat
lysoPAFAT
HGNC (Hugo) LPCAT1
LocusID (NCBI) 79888
Atlas_Id 52720
Location 5p15.33  [Link to chromosome band 5p15]
Location_base_pair Starts at 1461423 and ends at 1523977 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2017)		Data from Atlas, Mitelman, Cosmic Fusion, Fusion Cancer, TCGA fusion databases with official HUGO symbols (see references in chromosomal bands)
AP1S2 (Xp22.2) / LPCAT1 (5p15.33)ENTPD7 (10q24.2) / LPCAT1 (5p15.33)HAND2 (4q34.1) / LPCAT1 (5p15.33)
LPCAT1 (5p15.33) / CLPTM1L (5p15.33)LPCAT1 (5p15.33) / DAP (5p15.2)LPCAT1 (5p15.33) / ENTPD7 (10q24.2)
LPCAT1 (5p15.33) / SDHA (5p15.33)LPCAT1 (5p15.33) / SYT1 (12q21.2)TRIM25 (17q22) / LPCAT1 (5p15.33)
LPCAT1 5p15.33 / DAP 5p15.2LPCAT1 5p15.33 / SDHA 5p15.33

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 

Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 3 ]
  LPCAT1/CLPTM1L (5p15)
LPCAT1/DAP (5p15)
LPCAT1/SDHA (5p15)

External links

Nomenclature
HGNC (Hugo)LPCAT1   25718
Cards
Entrez_Gene (NCBI)LPCAT1  79888  lysophosphatidylcholine acyltransferase 1
AliasesAGPAT10; AGPAT9; AYTL2; LPCAT-1; 
PFAAP3; lpcat; lysoPAFAT
GeneCards (Weizmann)LPCAT1
Ensembl hg19 (Hinxton)ENSG00000153395 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000153395 [Gene_View]  ENSG00000153395 [Sequence]  chr5:1461423-1523977 [Contig_View]  LPCAT1 [Vega]
ICGC DataPortalENSG00000153395
TCGA cBioPortalLPCAT1
AceView (NCBI)LPCAT1
Genatlas (Paris)LPCAT1
WikiGenes79888
SOURCE (Princeton)LPCAT1
Genetics Home Reference (NIH)LPCAT1
Genomic and cartography
GoldenPath hg38 (UCSC)LPCAT1  -     chr5:1461423-1523977 -  5p15.33   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)LPCAT1  -     5p15.33   [Description]    (hg19-Feb_2009)
GoldenPathLPCAT1 - 5p15.33 [CytoView hg19]  LPCAT1 - 5p15.33 [CytoView hg38]
ImmunoBaseENSG00000153395
Mapping of homologs : NCBILPCAT1 [Mapview hg19]  LPCAT1 [Mapview hg38]
OMIM610472   
Gene and transcription
Genbank (Entrez)AB244719 AF052162 AF530061 AK022499 AK022505
RefSeq transcript (Entrez)NM_024830
RefSeq genomic (Entrez)NC_000005 NG_051622 NT_187547
Consensus coding sequences : CCDS (NCBI)LPCAT1
Cluster EST : UnigeneHs.368853 [ NCBI ]
CGAP (NCI)Hs.368853
Alternative Splicing GalleryENSG00000153395
Gene ExpressionLPCAT1 [ NCBI-GEO ]   LPCAT1 [ EBI - ARRAY_EXPRESS ]   LPCAT1 [ SEEK ]   LPCAT1 [ MEM ]
Gene Expression Viewer (FireBrowse)LPCAT1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevestigatorExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)79888
GTEX Portal (Tissue expression)LPCAT1
Human Protein AtlasENSG00000153395-LPCAT1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ8NF37   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ8NF37  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ8NF37
Splice isoforms : SwissVarQ8NF37
Catalytic activity : Enzyme2.3.1.67|2.3.1.23 [ Enzyme-Expasy ]   2.3.1.67|2.3.1.232.3.1.67|2.3.1.23 [ IntEnz-EBI ]   2.3.1.67|2.3.1.23 [ BRENDA ]   2.3.1.67|2.3.1.23 [ KEGG ]   
PhosPhoSitePlusQ8NF37
Domaine pattern : Prosite (Expaxy)EF_HAND_2 (PS50222)   
Domains : Interpro (EBI)EF-hand-dom_pair    EF_hand_dom    Plipid/glycerol_acylTrfase   
Domain families : Pfam (Sanger)Acyltransferase (PF01553)    EF-hand_8 (PF13833)   
Domain families : Pfam (NCBI)pfam01553    pfam13833   
Domain families : Smart (EMBL)EFh (SM00054)  PlsC (SM00563)  
Conserved Domain (NCBI)LPCAT1
DMDM Disease mutations79888
Blocks (Seattle)LPCAT1
SuperfamilyQ8NF37
Human Protein Atlas [tissue]ENSG00000153395-LPCAT1 [tissue]
Peptide AtlasQ8NF37
HPRD08572
IPIIPI00171626   
Protein Interaction databases
DIP (DOE-UCLA)Q8NF37
IntAct (EBI)Q8NF37
FunCoupENSG00000153395
BioGRIDLPCAT1
STRING (EMBL)LPCAT1
ZODIACLPCAT1
Ontologies - Pathways
QuickGOQ8NF37
Ontology : AmiGOGolgi membrane  calcium ion binding  endoplasmic reticulum  endoplasmic reticulum  endoplasmic reticulum membrane  Golgi apparatus  lipid droplet  plasma membrane  phosphatidic acid biosynthetic process  phosphatidylcholine biosynthetic process  phospholipid biosynthetic process  membrane  integral component of membrane  azurophil granule membrane  phosphatidylglycerol acyl-chain remodeling  phosphatidylcholine acyl-chain remodeling  phosphatidylcholine acyl-chain remodeling  surfactant homeostasis  neutrophil degranulation  positive regulation of protein catabolic process  1-alkenylglycerophosphocholine O-acyltransferase activity  1-acylglycerophosphocholine O-acyltransferase activity  1-acylglycerophosphocholine O-acyltransferase activity  1-alkylglycerophosphocholine O-acyltransferase activity  1-alkylglycerophosphocholine O-acetyltransferase activity  retina development in camera-type eye  negative regulation of phosphatidylcholine biosynthetic process  
Ontology : EGO-EBIGolgi membrane  calcium ion binding  endoplasmic reticulum  endoplasmic reticulum  endoplasmic reticulum membrane  Golgi apparatus  lipid droplet  plasma membrane  phosphatidic acid biosynthetic process  phosphatidylcholine biosynthetic process  phospholipid biosynthetic process  membrane  integral component of membrane  azurophil granule membrane  phosphatidylglycerol acyl-chain remodeling  phosphatidylcholine acyl-chain remodeling  phosphatidylcholine acyl-chain remodeling  surfactant homeostasis  neutrophil degranulation  positive regulation of protein catabolic process  1-alkenylglycerophosphocholine O-acyltransferase activity  1-acylglycerophosphocholine O-acyltransferase activity  1-acylglycerophosphocholine O-acyltransferase activity  1-alkylglycerophosphocholine O-acyltransferase activity  1-alkylglycerophosphocholine O-acetyltransferase activity  retina development in camera-type eye  negative regulation of phosphatidylcholine biosynthetic process  
Pathways : KEGGGlycerophospholipid metabolism    Ether lipid metabolism   
NDEx NetworkLPCAT1
Atlas of Cancer Signalling NetworkLPCAT1
Wikipedia pathwaysLPCAT1
Orthology - Evolution
OrthoDB79888
GeneTree (enSembl)ENSG00000153395
Phylogenetic Trees/Animal Genes : TreeFamLPCAT1
HOGENOMQ8NF37
Homologs : HomoloGeneLPCAT1
Homology/Alignments : Family Browser (UCSC)LPCAT1
Gene fusions - Rearrangements
Fusion : MitelmanLPCAT1/CLPTM1L [5p15.33/5p15.33]  
Fusion : MitelmanLPCAT1/DAP [5p15.33/5p15.2]  [t(5;5)(p15;p15)]  
Fusion : MitelmanLPCAT1/SDHA [5p15.33/5p15.33]  [t(5;5)(p15;p15)]  
Fusion PortalLPCAT1 5p15.33 DAP 5p15.2 KIRC
Fusion PortalLPCAT1 5p15.33 SDHA 5p15.33 LUAD
Fusion : QuiverLPCAT1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerLPCAT1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)LPCAT1
dbVarLPCAT1
ClinVarLPCAT1
1000_GenomesLPCAT1 
Exome Variant ServerLPCAT1
ExAC (Exome Aggregation Consortium)ENSG00000153395
GNOMAD BrowserENSG00000153395
Varsome BrowserLPCAT1
Genetic variants : HAPMAP79888
Genomic Variants (DGV)LPCAT1 [DGVbeta]
DECIPHERLPCAT1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisLPCAT1 
Mutations
ICGC Data PortalLPCAT1 
TCGA Data PortalLPCAT1 
Broad Tumor PortalLPCAT1
OASIS PortalLPCAT1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICLPCAT1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DLPCAT1
Mutations and Diseases : HGMDLPCAT1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch LPCAT1
DgiDB (Drug Gene Interaction Database)LPCAT1
DoCM (Curated mutations)LPCAT1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)LPCAT1 (select a term)
intoGenLPCAT1
Cancer3DLPCAT1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM610472   
Orphanet
DisGeNETLPCAT1
MedgenLPCAT1
Genetic Testing Registry LPCAT1
NextProtQ8NF37 [Medical]
TSGene79888
GENETestsLPCAT1
Target ValidationLPCAT1
Huge Navigator LPCAT1 [HugePedia]
snp3D : Map Gene to Disease79888
BioCentury BCIQLPCAT1
ClinGenLPCAT1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD79888
Chemical/Pharm GKB GenePA162394232
Clinical trialLPCAT1
Miscellaneous
canSAR (ICR)LPCAT1 (select the gene name)
DataMed IndexLPCAT1
Probes
Litterature
PubMed56 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineLPCAT1
EVEXLPCAT1
GoPubMedLPCAT1
iHOPLPCAT1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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© Atlas of Genetics and Cytogenetics in Oncology and Haematology
indexed on : Wed Nov 13 17:51:46 CET 2019
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