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PLOD1 (procollagen-lysine,2-oxoglutarate 5-dioxygenase 1)

Identity

Alias_namesLLH
PLOD
procollagen-lysine 1
Alias_symbol (synonym)LH1
Other aliasEDS6
LH
HGNC (Hugo) PLOD1
LocusID (NCBI) 5351
Atlas_Id 41749
Location 1p36.22  [Link to chromosome band 1p36]
Location_base_pair Starts at 11934667 and ends at 11975542 bp from pter ( according to hg38-Dec_2013)
Fusion genes
(updated 2016)
CLIC4 (1p36.11) / PLOD1 (1p36.22)MFN2 (1p36.22) / PLOD1 (1p36.22)PLOD1 (1p36.22) / TUBB (6p21.33)
RMI2 (16p13.13) / PLOD1 (1p36.22)TMEM208 (16q22.1) / PLOD1 (1p36.22)CLIC4 1p36.11 / PLOD1 1p36.22
MFN2 1p36.22 / PLOD1 1p36.22

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)PLOD1   9081
Cards
Entrez_Gene (NCBI)PLOD1  5351  procollagen-lysine,2-oxoglutarate 5-dioxygenase 1
AliasesEDS6; LH; LH1; LLH; 
PLOD
GeneCards (Weizmann)PLOD1
Ensembl hg19 (Hinxton)ENSG00000083444 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000083444 [Gene_View]  chr1:11934667-11975542 [Contig_View]  PLOD1 [Vega]
ICGC DataPortalENSG00000083444
TCGA cBioPortalPLOD1
AceView (NCBI)PLOD1
Genatlas (Paris)PLOD1
WikiGenes5351
SOURCE (Princeton)PLOD1
Genetics Home Reference (NIH)PLOD1
Genomic and cartography
GoldenPath hg38 (UCSC)PLOD1  -     chr1:11934667-11975542 +  1p36.22   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PLOD1  -     1p36.22   [Description]    (hg19-Feb_2009)
EnsemblPLOD1 - 1p36.22 [CytoView hg19]  PLOD1 - 1p36.22 [CytoView hg38]
Mapping of homologs : NCBIPLOD1 [Mapview hg19]  PLOD1 [Mapview hg38]
OMIM153454   225400   
Gene and transcription
Genbank (Entrez)AI347587 AK124035 AK294688 AK295254 AK299150
RefSeq transcript (Entrez)NM_000302 NM_001316320
RefSeq genomic (Entrez)
Consensus coding sequences : CCDS (NCBI)PLOD1
Cluster EST : UnigeneHs.75093 [ NCBI ]
CGAP (NCI)Hs.75093
Alternative Splicing GalleryENSG00000083444
Gene ExpressionPLOD1 [ NCBI-GEO ]   PLOD1 [ EBI - ARRAY_EXPRESS ]   PLOD1 [ SEEK ]   PLOD1 [ MEM ]
Gene Expression Viewer (FireBrowse)PLOD1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)5351
GTEX Portal (Tissue expression)PLOD1
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ02809   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ02809  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ02809
Splice isoforms : SwissVarQ02809
PhosPhoSitePlusQ02809
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)PLOD1
DMDM Disease mutations5351
Blocks (Seattle)PLOD1
SuperfamilyQ02809
Human Protein AtlasENSG00000083444
Peptide AtlasQ02809
HPRD01086
IPIIPI00943008   IPI01012138   IPI00027192   IPI00641236   IPI00643385   
Protein Interaction databases
DIP (DOE-UCLA)Q02809
IntAct (EBI)Q02809
FunCoupENSG00000083444
BioGRIDPLOD1
STRING (EMBL)PLOD1
ZODIACPLOD1
Ontologies - Pathways
QuickGOQ02809
Ontology : AmiGOresponse to hypoxia  iron ion binding  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  epidermis development  epidermis development  peptidyl-lysine hydroxylation  peptidyl-lysine hydroxylation  rough endoplasmic reticulum membrane  L-ascorbic acid binding  procollagen glucosyltransferase activity  protein homodimerization activity  hydroxylysine biosynthetic process  hydroxylysine biosynthetic process  hydroxylysine biosynthetic process  oxidation-reduction process  extracellular exosome  
Ontology : EGO-EBIresponse to hypoxia  iron ion binding  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  epidermis development  epidermis development  peptidyl-lysine hydroxylation  peptidyl-lysine hydroxylation  rough endoplasmic reticulum membrane  L-ascorbic acid binding  procollagen glucosyltransferase activity  protein homodimerization activity  hydroxylysine biosynthetic process  hydroxylysine biosynthetic process  hydroxylysine biosynthetic process  oxidation-reduction process  extracellular exosome  
Pathways : KEGGLysine degradation   
NDEx NetworkPLOD1
Atlas of Cancer Signalling NetworkPLOD1
Wikipedia pathwaysPLOD1
Orthology - Evolution
OrthoDB5351
GeneTree (enSembl)ENSG00000083444
Phylogenetic Trees/Animal Genes : TreeFamPLOD1
HOVERGENQ02809
HOGENOMQ02809
Homologs : HomoloGenePLOD1
Homology/Alignments : Family Browser (UCSC)PLOD1
Gene fusions - Rearrangements
Fusion : MitelmanCLIC4/PLOD1 [1p36.11/1p36.22]  [t(1;1)(p36;p36)]  
Fusion : MitelmanMFN2/PLOD1 [1p36.22/1p36.22]  [t(1;1)(p36;p36)]  
Fusion: TCGACLIC4 1p36.11 PLOD1 1p36.22 GBM
Fusion: TCGAMFN2 1p36.22 PLOD1 1p36.22 OV
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPLOD1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PLOD1
dbVarPLOD1
ClinVarPLOD1
1000_GenomesPLOD1 
Exome Variant ServerPLOD1
ExAC (Exome Aggregation Consortium)PLOD1 (select the gene name)
Genetic variants : HAPMAP5351
Genomic Variants (DGV)PLOD1 [DGVbeta]
DECIPHERPLOD1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPLOD1 
Mutations
ICGC Data PortalPLOD1 
TCGA Data PortalPLOD1 
Broad Tumor PortalPLOD1
OASIS PortalPLOD1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPLOD1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPLOD1
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
LOVD (Leiden Open Variation Database)Ehlers Danlos Syndrome Variant Database
BioMutasearch PLOD1
DgiDB (Drug Gene Interaction Database)PLOD1
DoCM (Curated mutations)PLOD1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PLOD1 (select a term)
intoGenPLOD1
Cancer3DPLOD1(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM153454    225400   
Orphanet4043   
MedgenPLOD1
Genetic Testing Registry PLOD1
NextProtQ02809 [Medical]
TSGene5351
GENETestsPLOD1
Target ValidationPLOD1
Huge Navigator PLOD1 [HugePedia]
snp3D : Map Gene to Disease5351
BioCentury BCIQPLOD1
ClinGenPLOD1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5351
Chemical/Pharm GKB GenePA33411
Clinical trialPLOD1
Miscellaneous
canSAR (ICR)PLOD1 (select the gene name)
Probes
Litterature
PubMed60 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePLOD1
EVEXPLOD1
GoPubMedPLOD1
iHOPPLOD1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Mon Sep 25 19:25:17 CEST 2017

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