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PLOD2 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 2)

Identity

Alias (NCBI)BRKS2
LH2
TLH
HGNC (Hugo) PLOD2
HGNC Alias symbLH2
HGNC Alias namelysyl hydroxlase 2
 procollagen-lysine 5-dioxygenase
HGNC Previous nameprocollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2
 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2
LocusID (NCBI) 5352
Atlas_Id 53907
Location 3q24  [Link to chromosome band 3q24]
Location_base_pair Starts at 146069441 and ends at 146161184 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)
PLOD2 (3q24) / ABCG1 (21q22.3)PLOD2 (3q24) / PLOD2 (3q24)PLOD2 (3q24) / PLSCR4 (3q24)
PLOD2 3q24 / ABCG1 21q22.3PLOD2 3q24 / PLSCR4 3q24

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

 



External links

 

Nomenclature
HGNC (Hugo)PLOD2   9082
Cards
Entrez_Gene (NCBI)PLOD2    procollagen-lysine,2-oxoglutarate 5-dioxygenase 2
AliasesBRKS2; LH2; TLH
GeneCards (Weizmann)PLOD2
Ensembl hg19 (Hinxton)ENSG00000152952 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000152952 [Gene_View]  ENSG00000152952 [Sequence]  chr3:146069441-146161184 [Contig_View]  PLOD2 [Vega]
ICGC DataPortalENSG00000152952
TCGA cBioPortalPLOD2
AceView (NCBI)PLOD2
Genatlas (Paris)PLOD2
SOURCE (Princeton)PLOD2
Genetics Home Reference (NIH)PLOD2
Genomic and cartography
GoldenPath hg38 (UCSC)PLOD2  -     chr3:146069441-146161184 -  3q24   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PLOD2  -     3q24   [Description]    (hg19-Feb_2009)
GoldenPathPLOD2 - 3q24 [CytoView hg19]  PLOD2 - 3q24 [CytoView hg38]
ImmunoBaseENSG00000152952
Genome Data Viewer NCBIPLOD2 [Mapview hg19]  
OMIM601865   609220   
Gene and transcription
Genbank (Entrez)AB209879 AK125700 AK130098 AK295084 AL832238
RefSeq transcript (Entrez)NM_000935 NM_182943
Consensus coding sequences : CCDS (NCBI)PLOD2
Gene ExpressionPLOD2 [ NCBI-GEO ]   PLOD2 [ EBI - ARRAY_EXPRESS ]   PLOD2 [ SEEK ]   PLOD2 [ MEM ]
Gene Expression Viewer (FireBrowse)PLOD2 [ Firebrowse - Broad ]
GenevisibleExpression of PLOD2 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5352
GTEX Portal (Tissue expression)PLOD2
Human Protein AtlasENSG00000152952-PLOD2 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO00469   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO00469  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO00469
PhosPhoSitePlusO00469
Domaine pattern : Prosite (Expaxy)FE2OG_OXY (PS51471)    LYS_HYDROXYLASE (PS01325)   
Domains : Interpro (EBI)Nucleotide-diphossugar_trans    Oxoglu/Fe-dep_dioxygenase    Pro_4_hyd_alph    Procol_lys_dOase   
Domain families : Pfam (Sanger)2OG-FeII_Oxy (PF03171)   
Domain families : Pfam (NCBI)pfam03171   
Domain families : Smart (EMBL)P4Hc (SM00702)  
Conserved Domain (NCBI)PLOD2
SuperfamilyO00469
AlphaFold pdb e-kbO00469   
Human Protein Atlas [tissue]ENSG00000152952-PLOD2 [tissue]
HPRD03519
Protein Interaction databases
DIP (DOE-UCLA)O00469
IntAct (EBI)O00469
BioGRIDPLOD2
STRING (EMBL)PLOD2
ZODIACPLOD2
Ontologies - Pathways
QuickGOO00469
Ontology : AmiGOresponse to hypoxia  iron ion binding  endoplasmic reticulum  endoplasmic reticulum membrane  cellular protein modification process  protein O-linked glycosylation  procollagen-lysine 5-dioxygenase activity  procollagen-lysine 5-dioxygenase activity  procollagen-lysine 5-dioxygenase activity  peptidyl-lysine hydroxylation  peptidyl-lysine hydroxylation  peptidyl-lysine hydroxylation  collagen fibril organization  rough endoplasmic reticulum membrane  L-ascorbic acid binding  procollagen glucosyltransferase activity  hydroxylysine biosynthetic process  extracellular exosome  
Ontology : EGO-EBIresponse to hypoxia  iron ion binding  endoplasmic reticulum  endoplasmic reticulum membrane  cellular protein modification process  protein O-linked glycosylation  procollagen-lysine 5-dioxygenase activity  procollagen-lysine 5-dioxygenase activity  procollagen-lysine 5-dioxygenase activity  peptidyl-lysine hydroxylation  peptidyl-lysine hydroxylation  peptidyl-lysine hydroxylation  collagen fibril organization  rough endoplasmic reticulum membrane  L-ascorbic acid binding  procollagen glucosyltransferase activity  hydroxylysine biosynthetic process  extracellular exosome  
Pathways : KEGGLysine degradation   
NDEx NetworkPLOD2
Atlas of Cancer Signalling NetworkPLOD2
Wikipedia pathwaysPLOD2
Orthology - Evolution
OrthoDB5352
GeneTree (enSembl)ENSG00000152952
Phylogenetic Trees/Animal Genes : TreeFamPLOD2
Homologs : HomoloGenePLOD2
Homology/Alignments : Family Browser (UCSC)PLOD2
Gene fusions - Rearrangements
Fusion : MitelmanPLOD2/ABCG1 [3q24/21q22.3]  
Fusion : QuiverPLOD2
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPLOD2 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PLOD2
dbVarPLOD2
ClinVarPLOD2
MonarchPLOD2
1000_GenomesPLOD2 
Exome Variant ServerPLOD2
GNOMAD BrowserENSG00000152952
Varsome BrowserPLOD2
ACMGPLOD2 variants
VarityO00469
Genomic Variants (DGV)PLOD2 [DGVbeta]
DECIPHERPLOD2 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPLOD2 
Mutations
ICGC Data PortalPLOD2 
TCGA Data PortalPLOD2 
Broad Tumor PortalPLOD2
OASIS PortalPLOD2 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPLOD2  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DPLOD2
Mutations and Diseases : HGMDPLOD2
LOVD (Leiden Open Variation Database)[gene] [transcripts] [variants]
BioMutaPLOD2
DgiDB (Drug Gene Interaction Database)PLOD2
DoCM (Curated mutations)PLOD2
CIViC (Clinical Interpretations of Variants in Cancer)PLOD2
Cancer3DPLOD2
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM601865    609220   
Orphanet313   
DisGeNETPLOD2
MedgenPLOD2
Genetic Testing Registry PLOD2
NextProtO00469 [Medical]
GENETestsPLOD2
Target ValidationPLOD2
Huge Navigator PLOD2 [HugePedia]
ClinGenPLOD2
Clinical trials, drugs, therapy
MyCancerGenomePLOD2
Protein Interactions : CTDPLOD2
Pharm GKB GenePA33412
PharosO00469
Clinical trialPLOD2
Miscellaneous
canSAR (ICR)PLOD2
HarmonizomePLOD2
DataMed IndexPLOD2
Probes
Litterature
PubMed95 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
EVEXPLOD2
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Oct 4 15:25:45 CEST 2021

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