Atlas of Genetics and Cytogenetics in Oncology and Haematology

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PDXDC1 (pyridoxal dependent decarboxylase domain containing 1)

Identity

Alias (NCBI)LP8165
HGNC (Hugo) PDXDC1
HGNC Alias symbKIAA0251
LocusID (NCBI) 23042
Atlas_Id 71810
Location 16p13.11  [Link to chromosome band 16p13]
Location_base_pair Starts at 14974963 and ends at 15038330 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)
CSGALNACT2 (10q11.21) / PDXDC1 (16p13.11)FBXO34 (14q22.3) / PDXDC1 (16p13.11)HNRNPUL1 (19q13.2) / PDXDC1 (16p13.11)
KDM5A (12p13.33) / PDXDC1 (16p13.11)MFSD10 (4p16.3) / PDXDC1 (16p13.11)PDXDC1 (16p13.11) / AHCYL1 (1p13.3)
PDXDC1 (16p13.11) / BRK1 (3p25.3)PDXDC1 (16p13.11) / HS6ST2 (Xq26.2)PDXDC1 (16p13.11) / ICE1 (5p15.32)
PDXDC1 (16p13.11) / LMF1 (16p13.3)PDXDC1 (16p13.11) / MMP14 (14q11.2)PDXDC1 (16p13.11) / PDXDC1 (16p13.11)
PDXDC1 (16p13.11) / RP11-82O18.1 ()PDXDC1 (16p13.11) / SMARCC2 (12q13.2)PDXDC1 (16p13.11) / TUBGCP4 (15q15.3)
PDXDC1 (16p13.11) / UBE2I (16p13.3)PDXDC1 RP11-82O18.1PDXDC1 LMF1

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) [ 2 ]
  t(14;16)(q11;p13) PDXDC1/MMP14
PDXDC1/LMF1 (16p13)

External links

Nomenclature
HGNC (Hugo)PDXDC1   28995
Cards
Entrez_Gene (NCBI)PDXDC1    pyridoxal dependent decarboxylase domain containing 1
AliasesLP8165
GeneCards (Weizmann)PDXDC1
Ensembl hg19 (Hinxton)ENSG00000179889 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000179889 [Gene_View]  ENSG00000179889 [Sequence]  chr16:14974963-15038330 [Contig_View]  PDXDC1 [Vega]
ICGC DataPortalENSG00000179889
TCGA cBioPortalPDXDC1
AceView (NCBI)PDXDC1
Genatlas (Paris)PDXDC1
SOURCE (Princeton)PDXDC1
Genetics Home Reference (NIH)PDXDC1
Genomic and cartography
GoldenPath hg38 (UCSC)PDXDC1  -     chr16:14974963-15038330 +  16p13.11   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PDXDC1  -     16p13.11   [Description]    (hg19-Feb_2009)
GoldenPathPDXDC1 - 16p13.11 [CytoView hg19]  PDXDC1 - 16p13.11 [CytoView hg38]
ImmunoBaseENSG00000179889
genome Data Viewer NCBIPDXDC1 [Mapview hg19]  
OMIM614244   
Gene and transcription
Genbank (Entrez)AK025504 AK090552 AK295168 AK299111 AK299799
RefSeq transcript (Entrez)NM_001285444 NM_001285445 NM_001285447 NM_001285448 NM_001285449 NM_001285450 NM_001324019 NM_001324020 NM_001324021 NM_015027
RefSeq genomic (Entrez)NC_000016 NT_187607
Consensus coding sequences : CCDS (NCBI)PDXDC1
Alternative Splicing GalleryENSG00000179889
Gene ExpressionPDXDC1 [ NCBI-GEO ]   PDXDC1 [ EBI - ARRAY_EXPRESS ]   PDXDC1 [ SEEK ]   PDXDC1 [ MEM ]
Gene Expression Viewer (FireBrowse)PDXDC1 [ Firebrowse - Broad ]
GenevisibleExpression of PDXDC1 in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)23042
GTEX Portal (Tissue expression)PDXDC1
Human Protein AtlasENSG00000179889-PDXDC1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ6P996   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ6P996  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ6P996
Splice isoforms : SwissVarQ6P996
PhosPhoSitePlusQ6P996
Domains : Interpro (EBI)PyrdxlP-dep_de-COase    PyrdxlP-dep_Trfase    PyrdxlP-dep_Trfase_major   
Domain families : Pfam (Sanger)Pyridoxal_deC (PF00282)   
Domain families : Pfam (NCBI)pfam00282   
Conserved Domain (NCBI)PDXDC1
Blocks (Seattle)PDXDC1
SuperfamilyQ6P996
Human Protein Atlas [tissue]ENSG00000179889-PDXDC1 [tissue]
Peptide AtlasQ6P996
HPRD13789
IPIIPI00384689   IPI00384285   IPI00645809   IPI00908545   IPI01015210   IPI00329208   IPI01011550   
Protein Interaction databases
DIP (DOE-UCLA)Q6P996
IntAct (EBI)Q6P996
BioGRIDPDXDC1
STRING (EMBL)PDXDC1
ZODIACPDXDC1
Ontologies - Pathways
QuickGOQ6P996
Ontology : AmiGOameboidal-type cell migration  endoplasmic reticulum  Golgi apparatus  sphingolipid metabolic process  sphinganine-1-phosphate aldolase activity  carboxy-lyase activity  carboxylic acid metabolic process  sphingolipid catabolic process  pyridoxal phosphate binding  intracellular membrane-bounded organelle  cadherin binding  
Ontology : EGO-EBIameboidal-type cell migration  endoplasmic reticulum  Golgi apparatus  sphingolipid metabolic process  sphinganine-1-phosphate aldolase activity  carboxy-lyase activity  carboxylic acid metabolic process  sphingolipid catabolic process  pyridoxal phosphate binding  intracellular membrane-bounded organelle  cadherin binding  
NDEx NetworkPDXDC1
Atlas of Cancer Signalling NetworkPDXDC1
Wikipedia pathwaysPDXDC1
Orthology - Evolution
OrthoDB23042
GeneTree (enSembl)ENSG00000179889
Phylogenetic Trees/Animal Genes : TreeFamPDXDC1
HOGENOMQ6P996
Homologs : HomoloGenePDXDC1
Homology/Alignments : Family Browser (UCSC)PDXDC1
Gene fusions - Rearrangements
Fusion PortalPDXDC1 RP11-82O18.1
Fusion PortalPDXDC1 LMF1
Fusion : QuiverPDXDC1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPDXDC1 [hg38]
dbVarPDXDC1
ClinVarPDXDC1
MonarchPDXDC1
1000_GenomesPDXDC1 
Exome Variant ServerPDXDC1
GNOMAD BrowserENSG00000179889
Varsome BrowserPDXDC1
Genomic Variants (DGV)PDXDC1 [DGVbeta]
DECIPHERPDXDC1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPDXDC1 
Mutations
ICGC Data PortalPDXDC1 
TCGA Data PortalPDXDC1 
Broad Tumor PortalPDXDC1
OASIS PortalPDXDC1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPDXDC1  [overview]  [genome browser]  [tissue]  [distribution]  
Somatic Mutations in Cancer : COSMIC3DPDXDC1
Mutations and Diseases : HGMDPDXDC1
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch PDXDC1
DgiDB (Drug Gene Interaction Database)PDXDC1
DoCM (Curated mutations)PDXDC1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PDXDC1 (select a term)
intoGenPDXDC1
Cancer3DPDXDC1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM614244   
Orphanet
DisGeNETPDXDC1
MedgenPDXDC1
Genetic Testing Registry PDXDC1
NextProtQ6P996 [Medical]
GENETestsPDXDC1
Target ValidationPDXDC1
Huge Navigator PDXDC1 [HugePedia]
ClinGenPDXDC1
Clinical trials, drugs, therapy
MyCancerGenomePDXDC1
Protein Interactions : CTD
Pharm GKB GenePA162399182
Clinical trialPDXDC1
Miscellaneous
canSAR (ICR)PDXDC1 (select the gene name)
HarmonizomePDXDC1
DataMed IndexPDXDC1
Probes
Litterature
PubMed37 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePDXDC1
EVEXPDXDC1
GoPubMedPDXDC1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Sat Dec 5 17:22:14 CET 2020
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