PHF1 (PHD finger protein 1)

1. Identity

Alias_symbol (synonym)
General Information
TDRD19C
Other aliasPCL1
PHF2
hPHF1
HGNC (Hugo) PHF1
LocusID (NCBI) 5252
Atlas_Id 42976
Location 6p21.32  [Link to chromosome band 6p21]
Location_base_pair Starts at 33410996 and ends at 33416453 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)
AFF3 (2q11.2) / PHF1 (6p21.32)EP400 (12q24.33) / PHF1 (6p21.32)EPC1 (10p11.22) / PHF1 (6p21.32)
JAZF1 (7p15.2) / PHF1 (6p21.32)MEAF6 (1p34.3) / PHF1 (6p21.32)PHF1 (6p21.32) / PHF1 (6p21.32)
PHF1 (6p21.32) / SUSD6 (14q24.1)EPC1 PHF1JAZF1 PHF1
MEAF6 PHF1

2. DNA/RNA

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

 

3. Breakpoints

4. External links

Nomenclature
HGNC (Hugo)PHF1   8919
Cards
Entrez_Gene (NCBI)PHF1  5252  PHD finger protein 1
AliasesMTF2L2; PCL1; PHF2; TDRD19C; 
hPHF1
GeneCards (Weizmann)PHF1
Ensembl hg19 (Hinxton)ENSG00000112511 [Gene_View]
Ensembl hg38 (Hinxton)ENSG00000112511 [Gene_View] &nbspENSG00000112511 [Sequence]  chr6:33410996-33416453 [Contig_View]  PHF1 [Vega]
ICGC DataPortalENSG00000112511
TCGA cBioPortalPHF1
AceView (NCBI)PHF1
Genatlas (Paris)PHF1
WikiGenes5252
SOURCE (Princeton)PHF1
Genetics Home Reference (NIH)PHF1
Genomic and cartography
GoldenPath hg38 (UCSC)PHF1  -     chr6:33410996-33416453 +  6p21.32   [Description]    (hg38-Dec_2013)
GoldenPath hg19 (UCSC)PHF1  -     6p21.32   [Description]    (hg19-Feb_2009)
EnsemblPHF1 - 6p21.32 [CytoView hg19]  PHF1 - 6p21.32 [CytoView hg38]
Mapping of homologs : NCBIPHF1 [Mapview hg19]  PHF1 [Mapview hg38]
OMIM602881   
Gene and transcription
Genbank (Entrez)AF029678 AF052205 AK225913 AK295412 AK299162
RefSeq transcript (Entrez)NM_002636 NM_024165
RefSeq genomic (Entrez)NC_000006 NT_167249
Consensus coding sequences : CCDS (NCBI)PHF1
Cluster EST : UnigeneHs.166204 [ NCBI ]
CGAP (NCI)Hs.166204
Alternative Splicing GalleryENSG00000112511
Gene ExpressionPHF1 [ NCBI-GEO ]   PHF1 [ EBI - ARRAY_EXPRESS ]   PHF1 [ SEEK ]   PHF1 [ MEM ]
Gene Expression Viewer (FireBrowse)PHF1 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets] &nbsp [Normal Tissue Atlas] &nbsp[carcinoma Classsification] &nbsp[NCI60]
GenevestigatorExpression in : [tissues] &nbsp[cell-lines] &nbsp[cancer] &nbsp[perturbations] &nbsp
BioGPS (Tissue expression)5252
GTEX Portal (Tissue expression)PHF1
Human Protein AtlasENSG00000112511-PHF1 [pathology]   [cell]   [tissue]
Protein : pattern, domain, 3D structure
UniProt/SwissProtO43189   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO43189  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO43189
Splice isoforms : SwissVarO43189
PhosPhoSitePlusO43189
Domaine pattern : Prosite (Expaxy)ZF_PHD_1 (PS01359)    ZF_PHD_2 (PS50016)   
Domains : Interpro (EBI)Mtf2_C_dom    PHF1    Tudor    Zinc_finger_PHD-type_CS    Znf_FYVE_PHD    Znf_PHD    Znf_PHD-finger    Znf_RING/FYVE/PHD   
Domain families : Pfam (Sanger)Mtf2_C (PF14061)    PHD (PF00628)   
Domain families : Pfam (NCBI)pfam14061    pfam00628   
Domain families : Smart (EMBL)PHD (SM00249)  TUDOR (SM00333)  
Conserved Domain (NCBI)PHF1
DMDM Disease mutations5252
Blocks (Seattle)PHF1
PDB (RSDB)2E5P    2M0O    4HCZ    5XFN    5XFO    5XFP   
PDB Europe2E5P    2M0O    4HCZ    5XFN    5XFO    5XFP   
PDB (PDBSum)2E5P    2M0O    4HCZ    5XFN    5XFO    5XFP   
PDB (IMB)2E5P    2M0O    4HCZ    5XFN    5XFO    5XFP   
Structural Biology KnowledgeBase2E5P    2M0O    4HCZ    5XFN    5XFO    5XFP   
SCOP (Structural Classification of Proteins)2E5P    2M0O    4HCZ    5XFN    5XFO    5XFP   
CATH (Classification of proteins structures)2E5P    2M0O    4HCZ    5XFN    5XFO    5XFP   
SuperfamilyO43189
Human Protein Atlas [tissue]ENSG00000112511-PHF1 [tissue]
Peptide AtlasO43189
HPRD04195
IPIIPI00011231   IPI00064665   IPI00942685   IPI00791580   IPI00793390   IPI00981058   IPI00789723   IPI00973445   IPI00973419   IPI01009409   IPI00982442   IPI00981715   
Protein Interaction databases
DIP (DOE-UCLA)O43189
IntAct (EBI)O43189
FunCoupENSG00000112511
BioGRIDPHF1
STRING (EMBL)PHF1
ZODIACPHF1
Ontologies - Pathways
QuickGOO43189
Ontology : AmiGODNA-binding transcription factor activity  protein binding  nucleus  nucleoplasm  nucleoplasm  cytoplasm  centrosome  chromatin organization  cellular response to DNA damage stimulus  nucleosome binding  methylated histone binding  methylated histone binding  ESC/E(Z) complex  ESC/E(Z) complex  site of double-strand break  sequence-specific DNA binding  negative regulation of gene expression, epigenetic  positive regulation of transcription, DNA-templated  metal ion binding  negative regulation of histone H3-K27 methylation  positive regulation of histone H3-K27 methylation  positive regulation of histone H3-K27 methylation  
Ontology : EGO-EBIDNA-binding transcription factor activity  protein binding  nucleus  nucleoplasm  nucleoplasm  cytoplasm  centrosome  chromatin organization  cellular response to DNA damage stimulus  nucleosome binding  methylated histone binding  methylated histone binding  ESC/E(Z) complex  ESC/E(Z) complex  site of double-strand break  sequence-specific DNA binding  negative regulation of gene expression, epigenetic  positive regulation of transcription, DNA-templated  metal ion binding  negative regulation of histone H3-K27 methylation  positive regulation of histone H3-K27 methylation  positive regulation of histone H3-K27 methylation  
NDEx NetworkPHF1
Atlas of Cancer Signalling NetworkPHF1
Wikipedia pathwaysPHF1
Orthology - Evolution
OrthoDB5252
GeneTree (enSembl)ENSG00000112511
Phylogenetic Trees/Animal Genes : TreeFamPHF1
HOGENOMO43189
Homologs : HomoloGenePHF1
Homology/Alignments : Family Browser (UCSC)PHF1
Gene fusions - Rearrangements
Fusion : MitelmanEP400/PHF1 [12q24.33/6p21.32] &nbsp[t(6;12)(p21;q24)]  
Fusion : MitelmanEPC1/PHF1 [10p11.22/6p21.32] &nbsp[t(6;10;10)(p21;q22;p11)]  
Fusion : MitelmanJAZF1/PHF1 [7p15.2/6p21.32] &nbsp[t(6;7)(p21;p15)]  
Fusion : MitelmanMEAF6/PHF1 [1p34.3/6p21.32] &nbsp[t(1;6)(p34;p21)]  
Fusion : QuiverPHF1
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerPHF1 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)PHF1
dbVarPHF1
ClinVarPHF1
1000_GenomesPHF1 
Exome Variant ServerPHF1
ExAC (Exome Aggregation Consortium)ENSG00000112511
GNOMAD BrowserENSG00000112511
Varsome BrowserPHF1
Genetic variants : HAPMAP5252
Genomic Variants (DGV)PHF1 [DGVbeta]
DECIPHERPHF1 [patients]   [syndromes]   [variants]   [genes]  
CONAN: Copy Number AnalysisPHF1 
Mutations
ICGC Data PortalPHF1 
TCGA Data PortalPHF1 
Broad Tumor PortalPHF1
OASIS PortalPHF1 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICPHF1  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDPHF1
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 PHF1
DgiDB (Drug Gene Interaction Database)PHF1
DoCM (Curated mutations)PHF1 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)PHF1 (select a term)
intoGenPHF1
Cancer3DPHF1(select the gene name)
Impact of mutations[PolyPhen2] [Provean] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM602881   
Orphanet
DisGeNETPHF1
MedgenPHF1
Genetic Testing Registry PHF1
NextProtO43189 [Medical]
TSGene5252
GENETestsPHF1
Target ValidationPHF1
Huge Navigator PHF1 [HugePedia]
snp3D : Map Gene to Disease5252
BioCentury BCIQPHF1
ClinGenPHF1
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD5252
Chemical/Pharm GKB GenePA33259
Clinical trialPHF1
Miscellaneous
canSAR (ICR)PHF1 (select the gene name)
DataMed IndexPHF1
Probes
Litterature
PubMed44 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMinePHF1
EVEXPHF1
GoPubMedPHF1
iHOPPHF1
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Thu Jan 17 18:30:36 CET 2019

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