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Aliases for PHF12 Gene

Aliases for PHF12 Gene

  • PHD Finger Protein 12 2 3 5
  • PHD Factor 1 3 4
  • PF1 3 4
  • PHD Zinc Finger Transcription Factor 3
  • KIAA1523 4

External Ids for PHF12 Gene

Previous GeneCards Identifiers for PHF12 Gene

  • GC17M027084
  • GC17M027377
  • GC17M027378
  • GC17M024256
  • GC17M027232
  • GC17M023440

Summaries for PHF12 Gene

GeneCards Summary for PHF12 Gene

PHF12 (PHD Finger Protein 12) is a Protein Coding gene. Diseases associated with PHF12 include Spastic Paraplegia 23 and Chromosome 17Q11.2 Deletion Syndrome, 1.4-Mb. GO annotations related to this gene include phosphatidylinositol binding and transcription corepressor binding.

UniProtKB/Swiss-Prot for PHF12 Gene

  • Acts as a transcriptional repressor. Involved in recruitment of functional SIN3A complexes to DNA. Represses transcription at least in part through the activity of an associated histone deacetylase (HDAC). May also repress transcription in a SIN3A-independent manner through recruitment of functional AES complexes to DNA.

Gene Wiki entry for PHF12 Gene

Additional gene information for PHF12 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHF12 Gene

Genomics for PHF12 Gene

Regulatory Elements for PHF12 Gene


Enhancers around PHF12 on UCSC Golden Path with GeneCards custom track

Promoters for PHF12 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000092792 1071 4201 ZFP64 FEZF1 DMAP1 YY1 ZNF143 SP3 ZC3H11A NFYC MEF2D ZNF610

Genomic Location for PHF12 Gene

Chromosome:
17
Start:
28,905,247 bp from pter
End:
28,951,771 bp from pter
Size:
46,525 bases
Orientation:
Minus strand

Genomic View for PHF12 Gene

Genes around PHF12 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF12 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF12 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for PHF12 Gene

Proteins for PHF12 Gene

  • Protein details for PHF12 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96QT6-PHF12_HUMAN
    Recommended name:
    PHD finger protein 12
    Protein Accession:
    Q96QT6
    Secondary Accessions:
    • Q0VAI5
    • Q2TAK2
    • Q6ZML2
    • Q9BV34
    • Q9H7U9
    • Q9P205

    Protein attributes for PHF12 Gene

    Size:
    1004 amino acids
    Molecular mass:
    109698 Da
    Quaternary structure:
    • Isoform 2 interacts with SIN3A in a complex composed of HDAC1, SAP30 and SIN3A. Interacts with AES.

    Three dimensional structures from OCA and Proteopedia for PHF12 Gene

    Alternative splice isoforms for PHF12 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PHF12 Gene

Post-translational modifications for PHF12 Gene

  • Ubiquitination at posLast=751751
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for PHF12 Gene

Domains & Families for PHF12 Gene

Gene Families for PHF12 Gene

Suggested Antigen Peptide Sequences for PHF12 Gene

Graphical View of Domain Structure for InterPro Entry

Q96QT6

UniProtKB/Swiss-Prot:

PHF12_HUMAN :
  • The polybasic region (PBR) is responsive to the binding to phosphoinositides (PtdInsPs).
Domain:
  • The polybasic region (PBR) is responsive to the binding to phosphoinositides (PtdInsPs).
genes like me logo Genes that share domains with PHF12: view

Function for PHF12 Gene

Molecular function for PHF12 Gene

UniProtKB/Swiss-Prot Function:
Acts as a transcriptional repressor. Involved in recruitment of functional SIN3A complexes to DNA. Represses transcription at least in part through the activity of an associated histone deacetylase (HDAC). May also repress transcription in a SIN3A-independent manner through recruitment of functional AES complexes to DNA.

Phenotypes From GWAS Catalog for PHF12 Gene

Gene Ontology (GO) - Molecular Function for PHF12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA --
GO:0001106 RNA polymerase II transcription corepressor activity IDA 22048773
GO:0001222 transcription corepressor binding IEA --
GO:0003682 chromatin binding IBA --
GO:0005515 protein binding IPI 11390640
genes like me logo Genes that share ontologies with PHF12: view
genes like me logo Genes that share phenotypes with PHF12: view

Animal Model Products

CRISPR Products

miRNA for PHF12 Gene

miRTarBase miRNAs that target PHF12

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for PHF12 Gene

Localization for PHF12 Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF12 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 PHF12 gene
Compartment Confidence
nucleus 5
extracellular 2
cytosol 2
plasma membrane 1
cytoskeleton 1
mitochondrion 1
endoplasmic reticulum 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for PHF12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,IEA 11390640
GO:0005654 nucleoplasm IDA --
GO:0016580 Sin3 complex IDA 22048773
GO:0017053 transcriptional repressor complex IDA 11390640
genes like me logo Genes that share ontologies with PHF12: view

Pathways & Interactions for PHF12 Gene

SuperPathways for PHF12 Gene

No Data Available

Gene Ontology (GO) - Biological Process for PHF12 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000122 negative regulation of transcription from RNA polymerase II promoter IDA 22048773
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IEA --
GO:0045892 negative regulation of transcription, DNA-templated IDA 11390640
genes like me logo Genes that share ontologies with PHF12: view

No data available for Pathways by source and SIGNOR curated interactions for PHF12 Gene

Drugs & Compounds for PHF12 Gene

No Compound Related Data Available

Transcripts for PHF12 Gene

Unigene Clusters for PHF12 Gene

PHD finger protein 12:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for PHF12 Gene

ExUns: 1 ^ 2 ^ 3a · 3b · 3c ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10a · 10b · 10c · 10d · 10e ^ 11 ^ 12a · 12b ^ 13a · 13b ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^
SP1: - - - - - - - -
SP2: - - - - - - - - - - - - - -
SP3: -
SP4: - - -
SP5: - - - - - - - -
SP6: - - - -
SP7: - - -
SP8: - -
SP9: -
SP10:
SP11:
SP12:
SP13: - - - - - - - - - - -
SP14: - - - - -
SP15:

ExUns: 18a · 18b · 18c · 18d ^ 19a · 19b · 19c · 19d ^ 20 ^ 21 ^ 22 ^ 23 ^ 24
SP1:
SP2:
SP3: - - -
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11: - - - -
SP12: - -
SP13:
SP14:
SP15: -

Relevant External Links for PHF12 Gene

GeneLoc Exon Structure for
PHF12
ECgene alternative splicing isoforms for
PHF12

Expression for PHF12 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PHF12 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PHF12 Gene

This gene is overexpressed in Whole Blood (x5.2).

Protein differential expression in normal tissues from HIPED for PHF12 Gene

This gene is overexpressed in Retina (20.0), Islet of Langerhans (18.4), CD8 Tcells (14.9), and Placenta (11.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PHF12 Gene



Protein tissue co-expression partners for PHF12 Gene

NURSA nuclear receptor signaling pathways regulating expression of PHF12 Gene:

PHF12

SOURCE GeneReport for Unigene cluster for PHF12 Gene:

Hs.444173

Evidence on tissue expression from TISSUES for PHF12 Gene

  • Liver(4.3)
  • Skin(4.2)
  • Nervous system(2.9)
  • Muscle(2.7)
  • Heart(2.3)
  • Kidney(2.3)
  • Intestine(2.2)
genes like me logo Genes that share expression patterns with PHF12: view

Primer Products

No data available for mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for PHF12 Gene

Orthologs for PHF12 Gene

This gene was present in the common ancestor of animals.

Orthologs for PHF12 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia PHF12 33 34
  • 99.87 (n)
cow
(Bos Taurus)
Mammalia PHF12 33 34
  • 95.42 (n)
dog
(Canis familiaris)
Mammalia PHF12 33 34
  • 94.91 (n)
mouse
(Mus musculus)
Mammalia Phf12 33 16 34
  • 94.42 (n)
rat
(Rattus norvegicus)
Mammalia Phf12 33
  • 94.36 (n)
oppossum
(Monodelphis domestica)
Mammalia PHF12 34
  • 82 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia PHF12 34
  • 76 (a)
OneToOne
chicken
(Gallus gallus)
Aves PHF12 33 34
  • 79.5 (n)
lizard
(Anolis carolinensis)
Reptilia PHF12 34
  • 69 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia phf12 33
  • 70.1 (n)
African clawed frog
(Xenopus laevis)
Amphibia phf12-prov 33
zebrafish
(Danio rerio)
Actinopterygii phf12b 33 34
  • 61.04 (n)
phf12a 34
  • 57 (a)
OneToMany
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.4158 33
fruit fly
(Drosophila melanogaster)
Insecta CG3815 34
  • 31 (a)
OneToOne
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 36 (a)
OneToMany
CSA.5338 34
  • 27 (a)
OneToMany
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.6972 33
Species where no ortholog for PHF12 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)
  • worm (Caenorhabditis elegans)

Evolution for PHF12 Gene

ENSEMBL:
Gene Tree for PHF12 (if available)
TreeFam:
Gene Tree for PHF12 (if available)

Paralogs for PHF12 Gene

genes like me logo Genes that share paralogs with PHF12: view

No data available for Paralogs for PHF12 Gene

Variants for PHF12 Gene

Sequence variations from dbSNP and Humsavar for PHF12 Gene

SNP ID Clin Chr 17 pos Sequence Context AA Info Type
rs1000045083 -- 28,913,590(+) ACTAT(C/T)ACCTA intron-variant
rs1000294506 -- 28,939,632(+) CATAA(C/T)GCAGA intron-variant
rs1000336892 -- 28,946,134(+) CTCAG(-/AAAAAC)AAAAA intron-variant, upstream-variant-2KB
rs1000426230 -- 28,945,517(+) ATGCT(A/G)AGGTC intron-variant, upstream-variant-2KB
rs1000443880 -- 28,951,462(+) GCAAA(A/C)TTACC upstream-variant-2KB, utr-variant-5-prime

Structural Variations from Database of Genomic Variants (DGV) for PHF12 Gene

Variant ID Type Subtype PubMed ID
nsv457719 CNV loss 19166990
nsv574662 CNV loss 21841781
nsv833408 CNV loss 17160897

Variation tolerance for PHF12 Gene

Residual Variation Intolerance Score: 8.79% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 2.36; 41.86% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for PHF12 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHF12

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF12 Gene

Disorders for PHF12 Gene

MalaCards: The human disease database

(2) MalaCards diseases for PHF12 Gene - From: DISEASES

Disorder Aliases PubMed IDs
spastic paraplegia 23
  • hereditary spastic paraplegia 23
chromosome 17q11.2 deletion syndrome, 1.4-mb
  • chromosome 17q11.2 deletion syndrome, 1.4mb
- elite association - COSMIC cancer census association via MalaCards
Search PHF12 in MalaCards View complete list of genes associated with diseases

Relevant External Links for PHF12

Genetic Association Database (GAD)
PHF12
Human Genome Epidemiology (HuGE) Navigator
PHF12
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
PHF12
genes like me logo Genes that share disorders with PHF12: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PHF12 Gene

Publications for PHF12 Gene

  1. Pf1, a novel PHD zinc finger protein that links the TLE corepressor to the mSin3A-histone deacetylase complex. (PMID: 11390640) Yochum GS … Ayer DE (Molecular and cellular biology 2001) 2 3 4 60
  2. The polybasic region that follows the plant homeodomain zinc finger 1 of Pf1 is necessary and sufficient for specific phosphoinositide binding. (PMID: 16893883) Kaadige MR … Ayer DE (The Journal of biological chemistry 2006) 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. Role for the mortality factors MORF4, MRGX, and MRG15 in transcriptional repression via associations with Pf1, mSin3A, and Transducin-Like Enhancer of Split. (PMID: 12391155) Yochum GS … Ayer DE (Molecular and cellular biology 2002) 3 22 60

Products for PHF12 Gene

Sources for PHF12 Gene

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