PHF20

PHD finger protein 20, the group of PHD finger proteins|NSL histone acetyltransferase complex|Tudor domain containing

Basic information

Region (hg38): 20:35771973-35950370

Previous symbols: [ "C20orf104" ]

Links

ENSG00000025293 ∙ NCBI:51230 ∙ OMIM:610335 ∙ HGNC:16098 ∙ Uniprot:Q9BVI0 ∙ 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 PHF20 gene.

• Inborn genetic diseases (21 variants)
• not provided (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHF20 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					5	5
missense			21		1	22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding					1	1
Total	0	0	21	0	7

Variants in PHF20

This is a list of pathogenic ClinVar variants found in the PHF20 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-35801593-G-A		not specified	Uncertain significance (Jan 04, 2024)
20-35842676-C-T		not specified	Uncertain significance (Jul 17, 2023)
20-35847411-A-G		not specified	Uncertain significance (Jul 20, 2021)
20-35858376-G-C		not specified	Uncertain significance (Apr 22, 2022)
20-35863240-C-T			Benign (Oct 09, 2017)
20-35863296-C-A		not specified	Uncertain significance (Aug 16, 2022)
20-35863337-C-T		not specified	Uncertain significance (Mar 11, 2024)
20-35869446-T-C		not specified	Uncertain significance (Mar 23, 2022)
20-35869519-C-T		Short stature	Likely pathogenic (Nov 18, 2001)
20-35870979-C-T		not specified	Uncertain significance (Feb 28, 2023)
20-35871087-C-T		not specified	Uncertain significance (Jul 09, 2021)
20-35871682-G-T		not specified	Uncertain significance (Oct 29, 2021)
20-35871715-G-C		not specified	Uncertain significance (Jun 29, 2022)
20-35871757-A-G		not specified	Uncertain significance (Jul 09, 2021)
20-35871785-C-T		not specified	Uncertain significance (Mar 01, 2023)
20-35871796-C-G		not specified	Uncertain significance (Jan 16, 2024)
20-35899548-G-C		not specified	Uncertain significance (Mar 07, 2024)
20-35899556-G-A		not specified	Uncertain significance (Dec 20, 2021)
20-35899609-G-C		not specified	Uncertain significance (Dec 19, 2023)
20-35913291-A-T		not specified	Uncertain significance (Apr 18, 2023)
20-35914144-C-T		not specified	Uncertain significance (Oct 18, 2021)
20-35917475-T-G			Benign (Jun 18, 2018)
20-35917480-G-A			Benign (Jul 13, 2018)
20-35917484-A-T		not specified	Uncertain significance (Oct 02, 2023)
20-35917521-T-C			Benign (Jun 18, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHF20	protein_coding	protein_coding	ENST00000374012	17	178408

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00125	125732	0	14	125746	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.35	399	555	0.719	0.0000300	6681
Missense in Polyphen		105	179.73	0.5842		2215
Synonymous	1.58	185	215	0.862	0.0000119	1858
Loss of Function	5.66	7	50.3	0.139	0.00000251	647

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000905
Ashkenazi Jewish	0.000210	0.000198
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000626	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000382	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Methyllysine-binding protein, component of the MOF histone acetyltransferase protein complex. Not required for maintaining the global histone H4 'Lys-16' acetylation (H4K16ac) levels or locus specific histone acetylation, but instead works downstream in transcriptional regulation of MOF target genes (By similarity). As part of the NSL complex it may be involved in acetylation of nucleosomal histone H4 on several lysine residues. Contributes to methyllysine-dependent p53/TP53 stabilization and up-regulation after DNA damage. {ECO:0000250, ECO:0000269|PubMed:20018852, ECO:0000269|PubMed:22864287}.
• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Stabilization of p53;p53-Dependent G1 DNA Damage Response;p53-Dependent G1/S DNA damage checkpoint;G1/S DNA Damage Checkpoints;Chromatin modifying enzymes;Cell Cycle Checkpoints;HATs acetylate histones;Regulation of TP53 Degradation;Regulation of TP53 Expression and Degradation;Chromatin organization;Regulation of TP53 Activity through Association with Co-factors;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Cell Cycle (Consensus)

Recessive Scores

• pRec: 0.132

Intolerance Scores

• loftool: 0.407
• rvis_EVS: -0.55
• rvis_percentile_EVS: 19.86

Haploinsufficiency Scores

• pHI: 0.597
• hipred: Y
• hipred_score: 0.708
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.838

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phf20
• Phenotype: skeleton phenotype; immune system phenotype; 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); hematopoietic system phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;histone H4-K5 acetylation;histone H4-K8 acetylation;histone H4-K16 acetylation;regulation of signal transduction by p53 class mediator
• Cellular component: histone acetyltransferase complex;nucleoplasm;cytosol;nuclear membrane;MLL1 complex
• Molecular function: DNA-binding transcription factor activity, RNA polymerase II-specific;DNA binding;protein binding;histone acetyltransferase activity (H4-K5 specific);histone acetyltransferase activity (H4-K8 specific);metal ion binding;histone acetyltransferase activity (H4-K16 specific)