Free for academic non-profit institutions. Other users need a Commercial license

PHF21A Gene(Protein Coding)

PHD Finger Protein 21A

GCID:
GC11M054226
GIFtS:
49
Genes Participants
UDN Logo

Aliases for PHF21A Gene

Aliases for PHF21A Gene

  • PHD Finger Protein 21A 2 3 5
  • BRAF35-HDAC Complex Protein BHC80 3 4
  • BHC80a 3 4
  • BHC80 3 4
  • BRAF35/HDAC2 Complex (80 KDa) 3
  • KIAA1696 4
  • BM-006 3

External Ids for PHF21A Gene

Previous GeneCards Identifiers for PHF21A Gene

  • GC11M045911
  • GC11M045950
  • GC11M045657
  • GC11M047071
  • GC11M047918
  • GC11M050775
  • GC11M051570
  • GC11M052232
  • GC11M052892
  • GC11M053560

Summaries for PHF21A Gene

Entrez Gene Summary for PHF21A Gene

  • The PHF21A gene encodes BHC80, a component of a BRAF35 (MIM 605535)/histone deacetylase (HDAC; see MIM 601241) complex (BHC) that mediates repression of neuron-specific genes through the cis-regulatory element known as repressor element-1 (RE1) or neural restrictive silencer (NRS) (Hakimi et al., 2002 [PubMed 12032298]).[supplied by OMIM, Nov 2010]

GeneCards Summary for PHF21A Gene

PHF21A (PHD Finger Protein 21A) is a Protein Coding gene. Diseases associated with PHF21A include Potocki-Shaffer Syndrome and Parietal Foramina. Among its related pathways are Response to elevated platelet cytosolic Ca2+ and Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3. Gene Ontology (GO) annotations related to this gene include chromatin binding. An important paralog of this gene is PHF21B.

UniProtKB/Swiss-Prot for PHF21A Gene

  • Component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it may act as a scaffold. Inhibits KDM1A-mediated demethylation of Lys-4 of histone H3 in vitro, suggesting a role in demethylation regulation.

Gene Wiki entry for PHF21A Gene

Additional gene information for PHF21A Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for PHF21A Gene

Genomics for PHF21A Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for PHF21A Gene

Promoters and enhancers for PHF21A Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH11I046117 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 550.8 +0.8 791 6 HDGF SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 ZNF766 ZNF213 PHF21A AMBRA1 RPS10P19 ZNF408 LARGE2 CKAP5 LOC101928894 ENSG00000254653
GH11I046099 Enhancer 1.1 Ensembl ENCODE dbSUPER 12.1 +20.9 20917 2.6 HDAC1 IRF2 ZSCAN4 CDC5L NFATC1 IKZF2 RUNX3 SMARCA5 ZNF687 DPF2 PHF21A LARGE2 ENSG00000254653
GH11I046048 Enhancer 0.9 Ensembl ENCODE 10.8 +70.9 70886 3.5 PKNOX1 FEZF1 ZIC2 ZNF843 OSR2 GATA3 JUND PRDM6 ZNF366 POLR2A PHF21A LARGE2 ENSG00000254664 ENSG00000254653
GH11I046055 Enhancer 0.6 ENCODE 10.5 +65.9 65887 0.4 FOXA2 SAP130 HLF ZNF644 ATF2 NFIL3 ZNF629 SCRT2 CEBPA CREB1 PHF21A ENSG00000254653 LARGE2
GH11I046113 Enhancer 0.6 FANTOM5 2.9 +7.5 7517 0.2 SMARCA5 YBX3 ADNP ZSCAN4 MLLT1 ZSCAN29 NR2C2 LARGE2 AMBRA1 PHF21A ENSG00000254653
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around PHF21A on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the PHF21A gene promoter:

Genomic Locations for PHF21A Gene

Genomic Locations for PHF21A Gene
chr11:45,929,319-46,121,434
(GRCh38/hg38)
Size:
192,116 bases
Orientation:
Minus strand
chr11:45,950,870-46,142,985
(GRCh37/hg19)

Genomic View for PHF21A Gene

Genes around PHF21A on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
PHF21A Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for PHF21A Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for PHF21A Gene

Proteins for PHF21A Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for PHF21A Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96BD5-PF21A_HUMAN
    Recommended name:
    PHD finger protein 21A
    Protein Accession:
    Q96BD5
    Secondary Accessions:
    • D3DQP5
    • Q6AWA2
    • Q9C0G7
    • Q9H8V9
    • Q9HAK6
    • Q9NZE9

    Protein attributes for PHF21A Gene

    Size:
    680 amino acids
    Molecular mass:
    74854 Da
    Quaternary structure:
    • Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST and PHF21A/BHC80. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I. In the complex, it interacts directly with HDAC1, HDAC2, HMG20B/BRAF35, KDM1A and RCOR1/CoREST.
    SequenceCaution:
    • Sequence=AAF64262.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305}; Sequence=BAB21787.1; Type=Erroneous initiation; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for PHF21A Gene

    Alternative splice isoforms for PHF21A Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for PHF21A Gene

Protein Expression for PHF21A Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for PHF21A Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for PHF21A Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for PHF21A Gene

Domains & Families for PHF21A Gene

Gene Families for PHF21A Gene

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

Protein Domains for PHF21A Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for PHF21A Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with PHF21A: view

No data available for UniProtKB/Swiss-Prot for PHF21A Gene

Function for PHF21A Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for PHF21A Gene

UniProtKB/Swiss-Prot Function:
Component of the BHC complex, a corepressor complex that represses transcription of neuron-specific genes in non-neuronal cells. The BHC complex is recruited at RE1/NRSE sites by REST and acts by deacetylating and demethylating specific sites on histones, thereby acting as a chromatin modifier. In the BHC complex, it may act as a scaffold. Inhibits KDM1A-mediated demethylation of Lys-4 of histone H3 in vitro, suggesting a role in demethylation regulation.

Phenotypes From GWAS Catalog for PHF21A Gene

Gene Ontology (GO) - Molecular Function for PHF21A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000977 RNA polymerase II regulatory region sequence-specific DNA binding IBA --
GO:0003677 DNA binding IEA --
GO:0003682 chromatin binding IBA,IEA --
GO:0003712 transcription cofactor activity IBA --
GO:0004407 histone deacetylase activity TAS --
genes like me logo Genes that share ontologies with PHF21A: view
genes like me logo Genes that share phenotypes with PHF21A: view

Human Phenotype Ontology for PHF21A Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for PHF21A Gene

MGI Knock Outs for PHF21A:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

No data available for Enzyme Numbers (IUBMB) , Transcription Factor Targets and HOMER Transcription for PHF21A Gene

Localization for PHF21A Gene

Subcellular locations from UniProtKB/Swiss-Prot for PHF21A Gene

Nucleus.

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 PHF21A gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for PHF21A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000118 histone deacetylase complex IDA 15325272
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:1990391 DNA repair complex IDA 24217620
genes like me logo Genes that share ontologies with PHF21A: view

No data available for Subcellular locations from the Human Protein Atlas (HPA) for PHF21A Gene

Pathways & Interactions for PHF21A Gene

genes like me logo Genes that share pathways with PHF21A: view

Gene Ontology (GO) - Biological Process for PHF21A Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated IBA --
GO:0007596 blood coagulation TAS --
GO:0016569 covalent chromatin modification IEA --
GO:0016575 histone deacetylation IEA --
genes like me logo Genes that share ontologies with PHF21A: view

No data available for SIGNOR curated interactions for PHF21A Gene

Drugs & Compounds for PHF21A Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for PHF21A Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for PHF21A Gene

(50) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(274) Selected AceView cDNA sequences:
(21) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for PHF21A Gene

PHD finger protein 21A:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for PHF21A Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13a · 13b · 13c ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19 ^ 20 ^
SP1: - - - - - - -
SP2: - - - - - - - -
SP3: - - - - - - - - -
SP4: - - - - - - - - -
SP5: - - - -
SP6: - - -
SP7:
SP8:
SP9: -
SP10:

ExUns: 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26a · 26b · 26c
SP1: - -
SP2: - -
SP3:
SP4:
SP5:
SP6:
SP7: -
SP8:
SP9:
SP10:

Relevant External Links for PHF21A Gene

GeneLoc Exon Structure for
PHF21A
ECgene alternative splicing isoforms for
PHF21A

Expression for PHF21A Gene

Products:

  1. Primer
  2. Gene Expression Assay

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for PHF21A Gene

mRNA expression in normal human tissues for PHF21A Gene
mRNA expression by GTEx for PHF21A GenemRNA expression by BioGPS for PHF21A Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for PHF21A Gene

This gene is overexpressed in Whole Blood (x7.7).

Protein differential expression in normal tissues from HIPED for PHF21A Gene

This gene is overexpressed in Pancreas (61.2).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for PHF21A Gene



Protein tissue co-expression partners for PHF21A Gene

NURSA nuclear receptor signaling pathways regulating expression of PHF21A Gene:

PHF21A

SOURCE GeneReport for Unigene cluster for PHF21A Gene:

Hs.502458

mRNA Expression by UniProt/SwissProt for PHF21A Gene:

Q96BD5-PF21A_HUMAN
Tissue specificity: Highly expressed in brain. Expressed at much lower level in other tissues.

Evidence on tissue expression from TISSUES for PHF21A Gene

  • Nervous system(4.7)
  • Bone marrow(4.2)
  • Lung(2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for PHF21A Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
Systems:
  • integumentary
  • nervous
  • reproductive
  • skeletal muscle
  • skeleton
Regions:
Head and neck:
  • brain
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • skull
Thorax:
  • chest wall
  • clavicle
  • rib
  • rib cage
  • scapula
  • sternum
Pelvis:
  • pelvis
  • penis
Limb:
  • ankle
  • arm
  • digit
  • elbow
  • femur
  • fibula
  • finger
  • foot
  • forearm
  • hand
  • hip
  • humerus
  • knee
  • lower limb
  • radius
  • shin
  • shoulder
  • thigh
  • tibia
  • toe
  • ulna
  • upper limb
  • wrist
General:
  • hair
  • skin
  • spinal column
  • vertebrae
genes like me logo Genes that share expression patterns with PHF21A: view

Orthologs for PHF21A Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for PHF21A Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia PHF21A 33 34
  • 99.9 (n)
dog
(Canis familiaris)
 Mammalia PHF21A 33 34
  • 96.07 (n)
cow
(Bos Taurus)
 Mammalia PHF21A 33 34
  • 95.28 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia PHF21A 34
  • 95 (a)
 OneToOne
rat
(Rattus norvegicus)
 Mammalia Phf21a 33
  • 93.03 (n)
mouse
(Mus musculus)
 Mammalia Phf21a 33 16 34
  • 92.83 (n)
oppossum
(Monodelphis domestica)
 Mammalia PHF21A 34
  • 92 (a)
 OneToOne
chicken
(Gallus gallus)
 Aves PHF21A 33 34
  • 85.48 (n)
lizard
(Anolis carolinensis)
 Reptilia PHF21A 34
  • 87 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia phf21a 33
  • 76.85 (n)
zebrafish
(Danio rerio)
 Actinopterygii phf21ab 33 34
  • 66.77 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes RCO1 34
  • 10 (a)
 OneToMany
Species where no ortholog for PHF21A was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • 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 PHF21A Gene

ENSEMBL:
Gene Tree for PHF21A (if available)
TreeFam:
Gene Tree for PHF21A (if available)

Paralogs for PHF21A Gene

Paralogs for PHF21A Gene

(4) SIMAP similar genes for PHF21A Gene using alignment to 11 proteins:

genes like me logo Genes that share paralogs with PHF21A: view

Variants for PHF21A Gene

Products:

  1. SNP Genotyping and Copy Number Assay

Sequence variations from dbSNP and Humsavar for PHF21A Gene

SNP ID Clin Chr 11 pos Variation AA Info Type
rs35995547 benign, not specified 45,935,742(-) AAAAAAAAAAAAAAAAAAAAAAA/AAAAAAAAA/AAAAAAAAAAAAAAAAAA/AAAAAAAAAAAAAAAAAAA/AAAAAAAAAAAAAAAAAAAA/AAAAAAAAAAAAAAAAAAAAA/AAAAAAAAAAAAAAAAAAAAAA/AAAAAAAAAAAAAAAAAAAAAAAA intron_variant
rs1000017334 -- 46,024,830(-) G/A intron_variant
rs1000017605 -- 46,060,650(-) C/T intron_variant
rs1000059557 -- 46,064,630(-) C/A intron_variant
rs1000072370 -- 46,022,631(-) T/C intron_variant

Structural Variations from Database of Genomic Variants (DGV) for PHF21A Gene

Variant ID Type Subtype PubMed ID
esv24317 CNV gain 19812545
esv2511558 CNV deletion 19546169
esv2672569 CNV deletion 23128226
esv2744431 CNV deletion 23290073
esv3547697 CNV deletion 23714750
esv4928 CNV loss 18987735
esv8587 CNV loss 19470904
esv987535 CNV loss 20482838
nsv1070027 CNV deletion 25765185
nsv1070028 CNV deletion 25765185
nsv1113386 CNV deletion 24896259
nsv38731 CNV deletion 16902084
nsv475047 CNV novel sequence insertion 20440878
nsv516442 CNV loss 19592680
nsv522527 CNV loss 19592680
nsv523952 CNV gain 19592680
nsv554200 CNV gain 21841781
nsv951609 CNV duplication 24416366
nsv957182 CNV deletion 24416366
nsv972947 CNV duplication 23825009
nsv972948 CNV duplication 23825009

Variation tolerance for PHF21A Gene

Residual Variation Intolerance Score: 20.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.85; 83.58% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for PHF21A Gene

Human Gene Mutation Database (HGMD)
PHF21A
SNPedia medical, phenotypic, and genealogical associations of SNPs for
PHF21A

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for PHF21A Gene

Disorders for PHF21A Gene

MalaCards: The human disease database

(4) MalaCards diseases for PHF21A Gene - From: HGMD, Orphanet, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
potocki-shaffer syndrome
  • pss
parietal foramina
  • pfm
articulation disorder
  • articulation impairment
speech disorder
  • speech disorders
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for PHF21A

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with PHF21A: view

No data available for UniProtKB/Swiss-Prot and Genatlas for PHF21A Gene

Publications for PHF21A Gene

  1. A core-BRAF35 complex containing histone deacetylase mediates repression of neuronal-specific genes. (PMID: 12032298) Hakimi MA … Shiekhattar R (Proceedings of the National Academy of Sciences of the United States of America 2002) 2 3 4 58
  2. Prediction of the coding sequences of unidentified human genes. XIX. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. (PMID: 11214970) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4 58
  3. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  4. Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies. (PMID: 21102462) Elks CE … Murray A (Nature genetics 2010) 3 44 58
  5. The rest repression of the neurosecretory phenotype is negatively modulated by BHC80, a protein of the BRAF/HDAC complex. (PMID: 19439607) Klajn A … D'Alessandro R (The Journal of neuroscience : the official journal of the Society for Neuroscience 2009) 3 22 58

Products for PHF21A Gene

Sources for PHF21A Gene

Content
Loading form....