PHF2 PHD finger protein 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: PHF2provided by HGNC
Official Full Name: PHD finger protein 2provided by HGNC
Primary source: HGNC:HGNC:8920
See related: Ensembl:ENSG00000197724 MIM:604351; AllianceGenome:HGNC:8920
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: GRC5; KDM7C; JHDM1E; CENP-35
Summary: This gene encodes a protein which contains a zinc finger-like PHD (plant homeodomain) finger, distinct from other classes of zinc finger motifs, and a hydrophobic and highly conserved domain. The PHD finger shows the typical Cys4-His-Cys3 arrangement. PHD finger genes are thought to belong to a diverse group of transcriptional regulators possibly affecting eukaryotic gene expression by influencing chromatin structure. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in ovary (RPKM 14.2), endometrium (RPKM 13.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q22.31

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (93576584..93679587)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (105744005..105847110)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (96338866..96441869)

Chromosome 9 - NC_000009.12 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 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?

PHF2-mediated H3K9me balance orchestrates heterochromatin stability and neural progenitor proliferation.
Title: PHF2-mediated H3K9me balance orchestrates heterochromatin stability and neural progenitor proliferation.
Palmitoylation-driven PHF2 ubiquitination remodels lipid metabolism through the SREBP1c axis in hepatocellular carcinoma.
Title: Palmitoylation-driven PHF2 ubiquitination remodels lipid metabolism through the SREBP1c axis in hepatocellular carcinoma.
Circ_MBNL3 Restrains Hepatocellular Carcinoma Progression by Sponging miR-873-5p to Release PHF2.
Title: Circ_MBNL3 Restrains Hepatocellular Carcinoma Progression by Sponging miR-873-5p to Release PHF2.
HIF-1alpha-mediated augmentation of miRNA-18b-5p facilitates proliferation and metastasis in osteosarcoma through attenuation PHF2.
Title: HIF-1α-mediated augmentation of miRNA-18b-5p facilitates proliferation and metastasis in osteosarcoma through attenuation PHF2.
Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders.
Title: Genome-wide analysis of 53,400 people with irritable bowel syndrome highlights shared genetic pathways with mood and anxiety disorders.
PHF2 regulates homology-directed DNA repair by controlling the resection of DNA double strand breaks.
Title: PHF2 regulates homology-directed DNA repair by controlling the resection of DNA double strand breaks.
The HCF-1:ChREBP complex resides at lipogenic gene promoters, where HCF-1 regulates H3K4 trimethylation to prime recruitment of the Jumonji C domain-containing histone demethylase PHF2 for epigenetic activation of these promoters.. these findings define HCF-1's interaction with ChREBP as a previously unappreciated mechanism whereby glucose signals are both relayed to ChREBP and transmitted for epigenetic regulation
Title: HCF-1 Regulates De Novo Lipogenesis through a Nutrient-Sensitive Complex with ChREBP.
lower expression of PHF2 promoted hepatocellular carcinoma (HCC) cell migration and linked to worse overall survival in HCC patients. Finally, the negative correlation between miR-221 and PHF2 expression levels in HCC specimens was further confirmed.
Title: MiR-221 Promotes Hepatocellular Carcinoma Cells Migration via Targeting PHF2.
PHF2 is a negative epigenetic regulator of MK and erythroid differentiation.
Title: Epigenetic regulation of megakaryocytic and erythroid differentiation by PHF2 histone demethylase.
Our results demonstrate that the IKAROS promotes PHF2 expression, and suggest that PHF2 (low) expression works with the IKAROS gene deletion to drive oncogenesis of ALL
Title: Plant homeodomain finger protein 2 as a novel IKAROS target in acute lymphoblastic leukemia.

Submit: New GeneRIF Correction See all GeneRIFs (17)

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

Copy number response

Description
Copy number response Triplosensitivity No evidence available (Last evaluated 2019-02-27) ClinGen Genome Curation Page Haploinsufficency Little evidence for dosage pathogenicity (Last evaluated 2019-02-27) ClinGen Genome Curation PagePubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of PHD finger protein 2 (PHF2) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH44280 (e-PCR)
- UniSTS:49185

SHGC-153852 (e-PCR)
- UniSTS:177957

G54542 (e-PCR)
- UniSTS:140851

G60031 (e-PCR)
- UniSTS:137297

SHGC-146039 (e-PCR)
- UniSTS:174955

NoName (e-PCR)
- UniSTS:484044

RH65301 (e-PCR)
- UniSTS:84180

SHGC-148780 (e-PCR)
- UniSTS:173052

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables histone H3K9 demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables histone H4K20 demethylase activity	ISS Inferred from Sequence or Structural Similarity more info
NOT enables histone demethylase activity	IDA Inferred from Direct Assay more info	PubMed
enables iron ion binding	IDA Inferred from Direct Assay more info	PubMed
enables methylated histone binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription coactivator activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription coregulator activity	IBA Inferred from Biological aspect of Ancestor more info
enables zinc ion binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in liver development	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of rDNA heterochromatin formation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA-templated transcription	IEA Inferred from Electronic Annotation more info
involved_in protein demethylation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in transcription initiation-coupled chromatin remodeling	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in kinetochore	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: lysine-specific demethylase PHF2

Names: centromere protein 35; jumonji C domain-containing histone demethylase 1E

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.

Genomic

NG_047001.1 RefSeqGene

Range

4958..107961

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_005392.4 → NP_005383.3 lysine-specific demethylase PHF2

See identical proteins and their annotated locations for NP_005383.3

Status: REVIEWED

Source sequence(s)

AL353629, AL359181, AL834263, BQ716020, CB990295

Consensus CDS

CCDS35069.1

UniProtKB/Swiss-Prot

O75151, Q4VXG0, Q8N3K2, Q9Y6N4

Related

ENSP00000352185.4, ENST00000359246.9

Conserved Domains (3) summary

pfam02373
Location:236 → 336

JmjC; JmjC domain, hydroxylase

smart00558
Location:201 → 264

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

cd15554
Location:7 → 53

PHD_PHF2_like; PHD finger found in PHF2, PHF8 and KDM7

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

93576584..93679587

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005252051.3 → XP_005252108.1 lysine-specific demethylase PHF2 isoform X1

See identical proteins and their annotated locations for XP_005252108.1

Conserved Domains (3) summary

pfam02373
Location:236 → 336

JmjC; JmjC domain, hydroxylase

smart00558
Location:201 → 264

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

cd15554
Location:7 → 53

PHD_PHF2_like; PHD finger found in PHF2, PHF8 and KDM7
XM_006717143.3 → XP_006717206.1 lysine-specific demethylase PHF2 isoform X3

Conserved Domains (3) summary

smart00558
Location:201 → 263

JmjC; A domain family that is part of the cupin metalloenzyme superfamily

cd15554
Location:7 → 53

PHD_PHF2_like; PHD finger found in PHF2, PHF8 and KDM7

cl21464
Location:236 → 301

cupin_like; Conserved domain found in cupin and related proteins
XM_047423475.1 → XP_047279431.1 lysine-specific demethylase PHF2 isoform X4
XM_047423474.1 → XP_047279430.1 lysine-specific demethylase PHF2 isoform X2

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

105744005..105847110

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054363110.1 → XP_054219085.1 lysine-specific demethylase PHF2 isoform X1
XM_054363112.1 → XP_054219087.1 lysine-specific demethylase PHF2 isoform X3
XM_054363113.1 → XP_054219088.1 lysine-specific demethylase PHF2 isoform X4
XM_054363111.1 → XP_054219086.1 lysine-specific demethylase PHF2 isoform X2

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_024517.1: Suppressed sequence

Description

NM_024517.1: This RefSeq was temporarily suppressed because currently there are not sufficient data to support this transcript.