PHF2

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

Basic information

Region (hg38): 9:93576583-93679587

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.

• Inborn genetic diseases (46 variants)
• not provided (19 variants)
• PHF2-related condition (2 variants)
• Autism spectrum disorder (2 variants)
• Malignant tumor of prostate (1 variants)
• not specified (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.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				3	7	10
missense			49	3	2	54
nonsense						0
start loss						0
frameshift			2			2
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding				1	1	2
Total	0	0	51	7	11

Variants in PHF2

This is a list of pathogenic ClinVar variants found in the PHF2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-93576755-G-GGCGGC		PHF2-related disorder	Likely benign (May 28, 2019)
9-93576789-G-A		not specified	Uncertain significance (Aug 28, 2023)
9-93636422-C-T		not specified	Uncertain significance (Jan 11, 2023)
9-93636440-G-T		not specified	Uncertain significance (Dec 21, 2023)
9-93636470-G-A		not specified	Uncertain significance (Sep 20, 2023)
9-93636513-G-A		not specified	Uncertain significance (Dec 06, 2021)
9-93636532-T-A			Benign (Sep 11, 2018)
9-93645638-C-T			Benign (Jun 13, 2019)
9-93645649-G-A		not specified	Uncertain significance (Jul 13, 2022)
9-93645654-C-T		not specified	Benign (May 04, 2022)
9-93645671-G-A		PHF2-related disorder	Benign (Jun 28, 2019)
9-93645679-A-G		not specified	Uncertain significance (Jan 20, 2023)
9-93645701-C-T		PHF2-related disorder	Benign (Nov 12, 2019)
9-93645728-C-T		PHF2-related disorder	Likely benign (May 08, 2019)
9-93649114-G-T		not specified	Uncertain significance (Jan 03, 2024)
9-93649166-C-T		not specified	Uncertain significance (Aug 17, 2022)
9-93649173-G-A		not specified	Uncertain significance (Aug 02, 2022)
9-93649184-G-A		not specified	Uncertain significance (Nov 15, 2021)
9-93653294-T-C		not specified	Uncertain significance (Oct 12, 2022)
9-93653375-G-A		PHF2-related disorder	Benign/Likely benign (Jan 03, 2020)
9-93654442-G-A		PHF2-related disorder	Likely benign (May 13, 2019)
9-93654448-G-A		PHF2-related disorder	Benign (Jul 01, 2019)
9-93654477-G-T			Uncertain significance (Nov 10, 2023)
9-93654521-G-A		not specified	Uncertain significance (Mar 15, 2023)
9-93656517-C-G		not specified	Uncertain significance (Jan 25, 2023)

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
1.00	0.00000494	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

Haploinsufficiency Scores

• pHI: 0.453
• hipred: Y
• hipred_score: 0.583
• ghis: 0.598

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

Mouse Genome Informatics

• Gene name: Phf2
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype

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