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Aliases for PHF10 Gene

Aliases for PHF10 Gene

  • PHD Finger Protein 10 2 3 5
  • BRG1-Associated Factor 45a 3 4
  • BAF45A 3 4
  • XAP135 3 4
  • BRG1-Associated Factor, 45-KD, A 3
  • PHD Zinc Finger Protein XAP135 3

External Ids for PHF10 Gene

Previous GeneCards Identifiers for PHF10 Gene

  • GC06M169719
  • GC06M169860
  • GC06M169921
  • GC06M169845
  • GC06M170104
  • GC06M167523

Summaries for PHF10 Gene

Entrez Gene Summary for PHF10 Gene

  • This gene contains a predicted ORF that encodes a protein with two zinc finger domains. The function of the encoded protein is not known. Sequence analysis suggests that multiple alternatively spliced transcript variants are derived from this gene but the full-length nature of only two of them is known. These two splice variants encode different isoforms. A pseudogene for this gene is located on Xq28. [provided by RefSeq, Jul 2008]

GeneCards Summary for PHF10 Gene

PHF10 (PHD Finger Protein 10) is a Protein Coding gene. Diseases associated with PHF10 include Schwannomatosis and Heterotopia, Periventricular. An important paralog of this gene is DPF2.

UniProtKB/Swiss-Prot for PHF10 Gene

  • Involved in transcription activity regulation by chromatin remodeling. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and is required for the proliferation of neural progenitors. During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity).

Gene Wiki entry for PHF10 Gene

Additional gene information for PHF10 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHF10 Gene

Genomics for PHF10 Gene

Regulatory Elements for PHF10 Gene

Enhancers for PHF10 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH06H170400 0.9 ENCODE 13.9 -674.9 -674903 0 HDGF FOXA2 ARNT ZNF473 NFRKB YBX1 PLRG1 ZBTB40 ZEB1 TCF12 WDR27 TBP FAM120B ENSG00000266896 PDCD2 ERMARD TCTE3 ENSG00000272848 PHF10 ENSG00000232640
GH06H170222 1 Ensembl ENCODE 12.5 -499.2 -499206 3 FOXA2 PKNOX1 SIN3A MAX RAD21 YY1 E2F1 GATA3 POLR2A MCM3 ENSG00000266896 PDCD2 TBP PHF10 WDR27 PSMB1 ENSG00000225532 RPL12P23 LOC154449
GH06H170532 0.9 ENCODE dbSUPER 10.6 -810.1 -810086 5 HNRNPUL1 FOXA2 FOXA3 ATF2 POLR2A MBD1 HNF4A SUPT5H PDCD2 TBP ENSG00000266896 PHF10 FAM120B PSMB1 PIR48716 PIR55352
GH06H169371 0.8 ENCODE 11.1 +353.8 353815 1 ZNF146 ZSCAN4 ZNF76 CHD4 GLI4 CDC5L ZNF2 TCF12 ZNF547 SCRT2 WDR27 FAM120B ERMARD TCTE3 ENSG00000232640 PHF10 ENSG00000266896 LINC02519 PIR40323
GH06H169700 1.1 ENCODE 6.8 +23.2 23213 4 HDGF PKNOX1 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF143 ZNF207 WDR27 FAM120B TBP C6orf120 LINC02519 ENSG00000266896 PDCD2 PHF10 ENSG00000227704
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around PHF10 on UCSC Golden Path with GeneCards custom track

Promoters for PHF10 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000207226 1566 2801 PKNOX1 FOXA2 ARNT ZFP64 ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B

Genomic Location for PHF10 Gene

Chromosome:
6
Start:
169,703,905 bp from pter
End:
169,725,566 bp from pter
Size:
21,662 bases
Orientation:
Minus strand

Genomic View for PHF10 Gene

Genes around PHF10 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF10 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF10 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF10 Gene

Proteins for PHF10 Gene

  • Protein details for PHF10 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q8WUB8-PHF10_HUMAN
    Recommended name:
    PHD finger protein 10
    Protein Accession:
    Q8WUB8
    Secondary Accessions:
    • Q2YDA3
    • Q53HG8
    • Q9BXD2
    • Q9NV26

    Protein attributes for PHF10 Gene

    Size:
    498 amino acids
    Molecular mass:
    56051 Da
    Quaternary structure:
    • Component of neural progenitors-specific chromatin remodeling complex (npBAF complex) composed of at least, ARID1A/BAF250A or ARID1B/BAF250B, SMARCD1/BAF60A, SMARCD3/BAF60C, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A, SMARCB1/BAF47, SMARCC1/BAF155, SMARCE1/BAF57, SMARCC2/BAF170, PHF10/BAF45A, ACTL6A/BAF53A and actin. Interacts with ACTL6A/BAF53A, SMARCA2/BRM/BAF190B, SMARCA4/BRG1/BAF190A and PBRM1/BAF180 (By similarity).
    SequenceCaution:
    • Sequence=AAH20954.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAI10324.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=AAK27451.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=BAA91934.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=BAD96332.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAG33554.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305}; Sequence=CAI12316.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for PHF10 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PHF10 Gene

Post-translational modifications for PHF10 Gene

  • Ubiquitination at Lys168, Lys249, and posLast=267267
  • Modification sites at PhosphoSitePlus

Other Protein References for PHF10 Gene

No data available for DME Specific Peptides for PHF10 Gene

Domains & Families for PHF10 Gene

Gene Families for PHF10 Gene

HGNC:
Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for PHF10 Gene

Suggested Antigen Peptide Sequences for PHF10 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q8WUB8

UniProtKB/Swiss-Prot:

PHF10_HUMAN :
  • Belongs to the SAYP family.
Family:
  • Belongs to the SAYP family.
genes like me logo Genes that share domains with PHF10: view

Function for PHF10 Gene

Molecular function for PHF10 Gene

UniProtKB/Swiss-Prot Function:
Involved in transcription activity regulation by chromatin remodeling. Belongs to the neural progenitors-specific chromatin remodeling complex (npBAF complex) and is required for the proliferation of neural progenitors. During neural development a switch from a stem/progenitor to a post-mitotic chromatin remodeling mechanism occurs as neurons exit the cell cycle and become committed to their adult state. The transition from proliferating neural stem/progenitor cells to post-mitotic neurons requires a switch in subunit composition of the npBAF and nBAF complexes. As neural progenitors exit mitosis and differentiate into neurons, npBAF complexes which contain ACTL6A/BAF53A and PHF10/BAF45A, are exchanged for homologous alternative ACTL6B/BAF53B and DPF1/BAF45B or DPF3/BAF45C subunits in neuron-specific complexes (nBAF). The npBAF complex is essential for the self-renewal/proliferative capacity of the multipotent neural stem cells. The nBAF complex along with CREST plays a role regulating the activity of genes essential for dendrite growth (By similarity).

Phenotypes From GWAS Catalog for PHF10 Gene

Gene Ontology (GO) - Molecular Function for PHF10 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with PHF10: view
genes like me logo Genes that share phenotypes with PHF10: view

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PHF10
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PHF10 Gene

Localization for PHF10 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF10 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for PHF10 gene
Compartment Confidence
nucleus 5
cytosol 2
extracellular 1
mitochondrion 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PHF10 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA --
GO:0071564 npBAF complex ISS --
genes like me logo Genes that share ontologies with PHF10: view

Pathways & Interactions for PHF10 Gene

SuperPathways for PHF10 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PHF10 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0007399 nervous system development IEA --
genes like me logo Genes that share ontologies with PHF10: view

No data available for Pathways by source and SIGNOR curated interactions for PHF10 Gene

Drugs & Compounds for PHF10 Gene

No Compound Related Data Available

Transcripts for PHF10 Gene

Unigene Clusters for PHF10 Gene

PHD finger protein 10:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for PHF10
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for PHF10 Gene

ExUns: 1a · 1b ^ 2a · 2b ^ 3a · 3b ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b
SP1: - -
SP2:
SP3:
SP4:
SP5:

Relevant External Links for PHF10 Gene

GeneLoc Exon Structure for
PHF10
ECgene alternative splicing isoforms for
PHF10

Expression for PHF10 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PHF10 Gene

Protein differential expression in normal tissues from HIPED for PHF10 Gene

This gene is overexpressed in CD8 Tcells (19.7), Ovary (12.5), CD4 Tcells (9.3), and Peripheral blood mononuclear cells (7.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, and MOPED for PHF10 Gene



Protein tissue co-expression partners for PHF10 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of PHF10 Gene:

PHF10

SOURCE GeneReport for Unigene cluster for PHF10 Gene:

Hs.435933

Evidence on tissue expression from TISSUES for PHF10 Gene

  • Intestine(4.3)
  • Liver(4.3)
  • Muscle(4.3)
  • Skin(4.3)
  • Nervous system(3.9)
genes like me logo Genes that share expression patterns with PHF10: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PHF10 Gene

Orthologs for PHF10 Gene

This gene was present in the common ancestor of animals.

Orthologs for PHF10 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PHF10 33 34
  • 99.85 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia PHF10 34
  • 96 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia PHF10 34
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia PHF10 33 34
  • 92.41 (n)
rat
(Rattus norvegicus)
Mammalia Phf10 33
  • 92.11 (n)
mouse
(Mus musculus)
Mammalia Phf10 33 16 34
  • 91.73 (n)
cow
(Bos Taurus)
Mammalia PHF10 33 34
  • 90.65 (n)
chicken
(Gallus gallus)
Aves PHF10 33 34
  • 85.18 (n)
lizard
(Anolis carolinensis)
Reptilia PHF10 34
  • 90 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phf10 33
  • 77.97 (n)
Str.10792 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.16782 33
zebrafish
(Danio rerio)
Actinopterygii phf10 33 34
  • 72.84 (n)
zgc66233 33
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.12707 33
fruit fly
(Drosophila melanogaster)
Insecta e(y)3 34
  • 6 (a)
ManyToMany
worm
(Caenorhabditis elegans)
Secernentea phf-10 33 34
  • 47.57 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 34 (a)
OneToOne
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.105 33
Species where no ortholog for PHF10 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for PHF10 Gene

ENSEMBL:
Gene Tree for PHF10 (if available)
TreeFam:
Gene Tree for PHF10 (if available)

Paralogs for PHF10 Gene

Paralogs for PHF10 Gene

(1) SIMAP similar genes for PHF10 Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for PHF10 Gene

genes like me logo Genes that share paralogs with PHF10: view

Variants for PHF10 Gene

Sequence variations from dbSNP and Humsavar for PHF10 Gene

SNP ID Clin Chr 06 pos Sequence Context AA Info Type
rs1000023966 -- 169,704,969(+) CTAGG(A/G)ATGAA intron-variant, utr-variant-3-prime
rs1000370325 -- 169,719,573(+) CATCT(A/T)TTTAA intron-variant
rs1000541844 -- 169,724,943(+) GGCAC(A/T)GCGGG upstream-variant-2KB
rs1000588974 -- 169,723,341(+) ACAGA(C/G)TTCCG intron-variant
rs1000681942 -- 169,726,038(+) ACTAT(G/T)ACACC intron-variant, upstream-variant-2KB

Structural Variations from Database of Genomic Variants (DGV) for PHF10 Gene

Variant ID Type Subtype PubMed ID
dgv11076n54 CNV loss 21841781
dgv11077n54 CNV loss 21841781
dgv11078n54 CNV gain 21841781
dgv11079n54 CNV gain 21841781
esv24038 CNV loss 19812545
nsv1032232 CNV loss 25217958
nsv1074450 CNV deletion 25765185
nsv1112912 CNV deletion 24896259
nsv1119096 CNV deletion 24896259
nsv605499 CNV gain 21841781
nsv605508 CNV loss 21841781
nsv605509 CNV loss 21841781
nsv605511 CNV loss 21841781
nsv605524 CNV loss 21841781
nsv830872 CNV loss 17160897

Variation tolerance for PHF10 Gene

Residual Variation Intolerance Score: 22% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.31; 6.86% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PHF10 Gene

Human Gene Mutation Database (HGMD)
PHF10
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHF10

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF10 Gene

Disorders for PHF10 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PHF10 Gene - From: HGMD and DISEASES

Disorder Aliases PubMed IDs
schwannomatosis
  • schwannomatosis-1
heterotopia, periventricular
  • periventricular nodular heterotopia
- elite association - COSMIC cancer census association via MalaCards
Search PHF10 in MalaCards View complete list of genes associated with diseases

Relevant External Links for PHF10

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PHF10
genes like me logo Genes that share disorders with PHF10: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PHF10 Gene

Publications for PHF10 Gene

  1. Physical and genetic characterization reveals a pseudogene, an evolutionary junction, and unstable loci in distal Xq28. (PMID: 11827455) Aradhya S … Nelson DL (Genomics 2002) 2 3 4 60
  2. PHF10 is required for cell proliferation in normal and SV40-immortalized human fibroblast cells. (PMID: 20068294) Banga SS … Ozer HL (Cytogenetic and genome research 2009) 3 4 60
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 60
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 60
  5. The DNA sequence and analysis of human chromosome 6. (PMID: 14574404) Mungall AJ … Beck S (Nature 2003) 3 4 60

Products for PHF10 Gene

Sources for PHF10 Gene

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