PHF2

PHD finger protein 2, the group of MicroRNA protein coding host genes|Lysine demethylases|PHD finger proteins

Basic information

Region (hg38): 9:93576584-93679587

Links

ENSG00000197724 ∙ NCBI:5253 ∙ OMIM:604351 ∙ HGNC:8920 ∙ Uniprot:O75151 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PHF2 gene.

• not_specified (124 variants)
• not_provided (18 variants)
• PHF2-related_disorder (17 variants)
• Autism_spectrum_disorder (2 variants)
• Prostate_cancer (1 variants)
• Neurodevelopmental_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005392.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			6	12	8	26
missense			124	7	3	134
nonsense		1				1
start loss						0
frameshift			2			2
splice donor/acceptor (+/-2bp)			3			3
Total	0	1	135	19	11

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF2	protein_coding	protein_coding	ENST00000359246	22	103181

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		125732	0	15	125747	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.49	389	637	0.610	0.0000401	7112
Missense in Polyphen		1	5.9297	0.16864		44
Synonymous	0.00914	288	288	0.999	0.0000210	2129
Loss of Function	6.16	4	51.9	0.0771	0.00000253	642

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000214	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000323	0.000323
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000981	0.0000653
Other	0.000502	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lysine demethylase that demethylates both histones and non-histone proteins. Enzymatically inactive by itself, and becomes active following phosphorylation by PKA: forms a complex with ARID5B and mediates demethylation of methylated ARID5B. Demethylation of ARID5B leads to target the PHF2-ARID5B complex to target promoters, where PHF2 mediates demethylation of dimethylated 'Lys-9' of histone H3 (H3K9me2), followed by transcription activation of target genes. The PHF2-ARID5B complex acts as a coactivator of HNF4A in liver. PHF2 is recruited to trimethylated 'Lys-4' of histone H3 (H3K4me3) at rDNA promoters and promotes expression of rDNA. {ECO:0000269|PubMed:20129925, ECO:0000269|PubMed:21167174, ECO:0000269|PubMed:21532585}.
• Pathway: HDMs demethylate histones;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.352
• rvis_EVS: -1.03
• rvis_percentile_EVS: 7.86

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.226

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	Medium	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Gene ontology

• Biological process: liver development;protein demethylation;histone H3-K9 demethylation;oxidation-reduction process;negative regulation of chromatin silencing at rDNA
• Cellular component: kinetochore;condensed chromosome kinetochore;nucleus;nucleoplasm;nucleolus
• Molecular function: transcription coactivator activity;iron ion binding;protein binding;zinc ion binding;histone demethylase activity;histone demethylase activity (H3-K9 specific);methylated histone binding;dioxygenase activity