PHF20 PHD finger protein 20 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PHF20provided by HGNC
Official Full Name: PHD finger protein 20provided by HGNC
Primary source: HGNC:HGNC:16098
See related: Ensembl:ENSG00000025293 MIM:610335
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: NZF; TZP; GLEA2; HCA58; TDRD20A; C20orf104
Expression: Ubiquitous expression in testis (RPKM 8.8), brain (RPKM 8.0) and 25 other tissues See more
Orthologs: mouse all

Genomic context

Location:: 20q11.22-q11.23

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
109.20190905	current	GRCh38.p13 (GCF_000001405.39)	20	NC_000020.11 (35772003..35950372)
105	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (34359923..34538292)

Chromosome 20 - NC_000020.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

PHF20 interacts with poly(ADP-ribose) polymerase 1 (PARP1) and directly binds to promoter regions of octamer-binding transcription factor 4 (OCT4) and sex determining region Y-box 2 (SOX2) to modulate a histone mark associated with active transcription, trimethylation of lysine 4 on histone H3 protein subunit (H3K4me3).
Title: PHF20 collaborates with PARP1 to promote stemness and aggressiveness of neuroblastoma cells through activation of SOX2 and OCT4.
These findings establish a unique PHF20-mediated link between MOF histone acetyltransferase (HAT), p53, and dimethylated lysine 4 of histone H3, and suggest a model for rapid spreading of H4K16ac-enriched open chromatin.
Title: PHF20 Readers Link Methylation of Histone H3K4 and p53 with H4K16 Acetylation.
PHF20 may play an important role in Non-small-cell lung cancer (NSCLC).
Title: Expression of PHF20 protein contributes to good prognosis of NSCLC and is associated with Bax expression.
Along with the PHF20/MOF complex, G9a links the crosstalk between ERalpha methylation and histone acetylation that governs the epigenetic regulation of hormonal gene expression.
Title: G9a-mediated methylation of ERα links the PHF20/MOF histone acetyltransferase complex to hormonal gene expression.
suggests a del(20q)-independent decrease in PHF20 expression in primary myelofibrosis
Title: Altered expression of tumor suppressor PHF20 in myeloproliferative neoplasms.
Plant homeodomain finger protein 20 (PHF20) maintains NF-kappaB in an active state in the nucleus by inhibiting the interaction between PP2A and p65.
Title: PHF20 regulates NF-κB signalling by disrupting recruitment of PP2A to p65.
PHF20 is a novel substrate for PKB and its phosphorylation by PKB plays an important role in tumorigenesis via regulating of p53 mediated signaling.
Title: PKB-mediated PHF20 phosphorylation on Ser291 is required for p53 function in DNA damage.
Association with PHF20 promotes stabilization and activation of p53 by diminishing Mdm2-mediated p53 ubiquitylation and degradation.
Title: PHF20 is an effector protein of p53 double lysine methylation that stabilizes and activates p53.
Data report the crystal structures of the N-terminal Tudor domains of PHF20 and highlight the novel structural features of each domain.
Title: Crystal structures of the Tudor domains of human PHF20 reveal novel structural variations on the Royal Family of proteins.
genetic alterations of TSPAN14, SLC2A13 and PHF20 could play a role in non-small-cell lung cancer promotion
Title: Identification of genes associated with non-small-cell lung cancer promotion and progression.

Submit: New GeneRIF Correction See all GeneRIFs (12)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

NHGRI GWAS Catalog

Description
Genome-wide meta-analysis identifies new susceptibility loci for migraine. NHGRI GWA Catalog NHGRI GWA CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Pathways from BioSystems

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Chromatin modifying enzymes, organism-specific biosystem (from REACTOME)
Chromatin modifying enzymes, organism-specific biosystemEukaryotic DNA is associated with histone proteins and organized into a complex nucleoprotein structure called chromatin. This structure decreases the accessibility of DNA but also helps to protect i...
Chromatin organization, organism-specific biosystem (from REACTOME)
Chromatin organization, organism-specific biosystemChromatin organization refers to the composition and conformation of complexes between DNA, protein and RNA. It is determined by processes that result in the specification, formation or maintenance o...
Gene Expression, organism-specific biosystem (from REACTOME)
Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
Generic Transcription Pathway, organism-specific biosystem (from REACTOME)
Generic Transcription Pathway, organism-specific biosystemOVERVIEW OF TRANSCRIPTION REGULATION: Detailed studies of gene transcription regulation in a wide variety of eukaryotic systems has revealed the general principles and mechanisms by which cell- or t...
HATs acetylate histones, organism-specific biosystem (from REACTOME)
HATs acetylate histones, organism-specific biosystemHistone acetyltransferases (HATs) involved in histone modifications are referred to as A-type or nuclear HATs. They can be grouped into at least four families based on sequence conservation within th...
Regulation of TP53 Activity, organism-specific biosystem (from REACTOME)
Regulation of TP53 Activity, organism-specific biosystemProtein stability and transcriptional activity of TP53 (p53) tumor suppressor are regulated by post-translational modifications that include ubiquitination, phosphorylation, acetylation, methylation,...
Regulation of TP53 Activity through Association with Co-factors, organism-specific biosystem (from REACTOME)
Regulation of TP53 Activity through Association with Co-factors, organism-specific biosystemAssociation of TP53 (p53) with various transcriptional co-factors can promote, inhibit or provide specificity towards either transcription of cell cycle arrest genes or transcription of cell death ge...
Transcriptional Regulation by TP53, organism-specific biosystem (from REACTOME)
Transcriptional Regulation by TP53, organism-specific biosystemThe tumor suppressor TP53 (encoded by the gene p53) is a transcription factor. Under stress conditions, it recognizes specific responsive DNA elements and thus regulates the transcription of many gen...

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D20S564E (e-PCR)
- UniSTS:30735

GDB:434012 (e-PCR)
- UniSTS:157204

GDB:312794 (e-PCR)
- UniSTS:30247

L17705 (e-PCR)
- UniSTS:66091

D8S2278 (e-PCR)
- UniSTS:473906

D8S2279 (e-PCR)
- UniSTS:473907

D20S909 (e-PCR), detects polymorphism
- UniSTS:52022

RH98357 (e-PCR)
- UniSTS:85872

D1S1423 (e-PCR)
- UniSTS:149619

G60337 (e-PCR)
- UniSTS:137593

T03643 (e-PCR)
- UniSTS:17282

RH15995 (e-PCR)
- UniSTS:48010

D11S3114 (e-PCR)
- UniSTS:152207

L17877 (e-PCR)
- UniSTS:61334

AFM240wf8 (e-PCR)
- UniSTS:17075

Z94588 (e-PCR)
- UniSTS:53434

A003B07 (e-PCR)
- UniSTS:9923

RH107 (e-PCR)
- UniSTS:38851

D20S1058 (e-PCR)
- UniSTS:12763

D3S1673 (e-PCR)
- UniSTS:148450

Homology

Homologs of the PHF20 gene: The PHF20 gene is conserved in chimpanzee, Rhesus monkey, dog, cow, mouse, rat, chicken, and frog.
Orthologs from Annotation Pipeline: 252 organisms have orthologs with human gene PHF20
Orthologs

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
DNA binding	IEA Inferred from Electronic Annotation more info
DNA-binding transcription factor activity, RNA polymerase II-specific	ISM Inferred from Sequence Model more info	PubMed
contributes_to histone acetyltransferase activity (H4-K16 specific)	IBA Inferred from Biological aspect of Ancestor more info	PubMed
contributes_to histone acetyltransferase activity (H4-K16 specific)	IDA Inferred from Direct Assay more info	PubMed
contributes_to histone acetyltransferase activity (H4-K5 specific)	IBA Inferred from Biological aspect of Ancestor more info	PubMed
contributes_to histone acetyltransferase activity (H4-K5 specific)	IDA Inferred from Direct Assay more info	PubMed
contributes_to histone acetyltransferase activity (H4-K8 specific)	IBA Inferred from Biological aspect of Ancestor more info	PubMed
contributes_to histone acetyltransferase activity (H4-K8 specific)	IDA Inferred from Direct Assay more info	PubMed
metal ion binding	IEA Inferred from Electronic Annotation more info
protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
histone H4-K16 acetylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
histone H4-K16 acetylation	IDA Inferred from Direct Assay more info	PubMed
histone H4-K5 acetylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
histone H4-K5 acetylation	IDA Inferred from Direct Assay more info	PubMed
histone H4-K8 acetylation	IBA Inferred from Biological aspect of Ancestor more info	PubMed
histone H4-K8 acetylation	IDA Inferred from Direct Assay more info	PubMed
regulation of signal transduction by p53 class mediator	TAS Traceable Author Statement more info
regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
MLL1 complex	IDA Inferred from Direct Assay more info	PubMed
cytosol	IDA Inferred from Direct Assay more info
cytosol	TAS Traceable Author Statement more info
histone acetyltransferase complex	IBA Inferred from Biological aspect of Ancestor more info	PubMed
histone acetyltransferase complex	IDA Inferred from Direct Assay more info	PubMed
nuclear membrane	IDA Inferred from Direct Assay more info
nucleoplasm	IDA Inferred from Direct Assay more info
nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: PHD finger protein 20

Names: glioma-expressed antigen 2; hepatocellular carcinoma-associated antigen 58; novel zinc finger protein; transcription factor TZP; tudor domain containing 20A

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_016436.5 → NP_057520.2 PHD finger protein 20

See identical proteins and their annotated locations for NP_057520.2

Status: VALIDATED

Source sequence(s)

AL109965, AL137330, AY027523, BC093405

Consensus CDS

CCDS13268.1

UniProtKB/Swiss-Prot

Q9BVI0

Related

ENSP00000363124.3, ENST00000374012.8

Conserved Domains (4) summary

cd04508
Location:90 → 135

TUDOR; Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to ...

cd15634
Location:654 → 697

PHD_PHF20; PHD finger found in PHD finger protein 20 (PHF20)

pfam12618
Location:176 → 259

DUF3776; Protein of unknown function (DUF3776)

cl17705
Location:3 → 68

MBT; mbt repeat

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

NC_000020.11 Reference GRCh38.p13 Primary Assembly

Range

35772003..35950372

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017027869.2 → XP_016883358.1 PHD finger protein 20 isoform X2

Conserved Domains (2) summary

cd15634
Location:538 → 581

PHD_PHF20; PHD finger found in PHD finger protein 20 (PHF20)

pfam10243
Location:28 → 197

MIP-T3; Microtubule-binding protein MIP-T3
XM_011528843.2 → XP_011527145.1 PHD finger protein 20 isoform X3

See identical proteins and their annotated locations for XP_011527145.1

Conserved Domains (1) summary

cl22851
Location:251 → 294

PHD_SF; PHD finger superfamily
XM_024451890.1 → XP_024307658.1 PHD finger protein 20 isoform X4

Conserved Domains (1) summary

cl22851
Location:182 → 225

PHD_SF; PHD finger superfamily
XM_017027871.2 → XP_016883360.1 PHD finger protein 20 isoform X3

Conserved Domains (1) summary

cl22851
Location:251 → 294

PHD_SF; PHD finger superfamily
XM_017027868.2 → XP_016883357.1 PHD finger protein 20 isoform X1
XM_017027870.2 → XP_016883359.1 PHD finger protein 20 isoform X2

Conserved Domains (2) summary

cd15634
Location:538 → 581

PHD_PHF20; PHD finger found in PHD finger protein 20 (PHF20)

pfam10243
Location:28 → 197

MIP-T3; Microtubule-binding protein MIP-T3
XM_024451889.1 → XP_024307657.1 PHD finger protein 20 isoform X2

Conserved Domains (2) summary

cd15634
Location:538 → 581

PHD_PHF20; PHD finger found in PHD finger protein 20 (PHF20)

pfam10243
Location:28 → 197

MIP-T3; Microtubule-binding protein MIP-T3
XM_005260421.3 → XP_005260478.1 PHD finger protein 20 isoform X3

See identical proteins and their annotated locations for XP_005260478.1

Conserved Domains (1) summary

cl22851
Location:251 → 294

PHD_SF; PHD finger superfamily
XM_011528844.2 → XP_011527146.1 PHD finger protein 20 isoform X3

See identical proteins and their annotated locations for XP_011527146.1

Conserved Domains (1) summary

cl22851
Location:251 → 294

PHD_SF; PHD finger superfamily