PHF20

protein-coding

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

Gene summary

Predicted to enable DNA binding activity and zinc ion binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Located in nuclear membrane and nucleoplasm. Part of MLL1 complex and histone acetyltransferase complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

C20orf104

MANE transcript

NM_016436.5

Inheritance

—

ClinVar variants

P:2U:116B:8

Top phenotype

Short stature

gnomAD constraint

pLI —, LoF o/e 0.14

Max pathogenic AF

—

Genomic locus

chr20:35,771,974-35,950,370

External References & Databases

Ensembl (ENSG00000025293)

Transcript & Mutation Effects

hg38 • Region Span ~178.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PHF20 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 104

not providedTotal: 12

Short statureTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016436.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar		5 clinvar	7
missense		2 clinvar	107 clinvar	2 clinvar	1 clinvar	112
nonsense			3 clinvar			3
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	2	116	2	6	126

Highest pathogenic variant AF is 0.0000068405066

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016436.5	RefSeq	NP_057520.2	17	MANE Select
ENST00000374012.8	Ensembl	ENSP00000363124.3	17	MANE Select
ENST00000339089.10	Ensembl	ENSP00000341900.6	10	Standard
ENST00000374000.8	Ensembl	ENSP00000363112.4	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription
Stabilization of p53
p53-Dependent G1 DNA Damage Response

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

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)

Cellular Component

histone acetyltransferase complex
nucleoplasm
cytosol
nuclear membrane
MLL1 complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000374012
Coding exons: 17
Length: 178408
Individuals with no LoFs: 125732
Homozygous LoFs: 0
Heterozygous LoFs: 14
Defined: 125746
p: 0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.35	399	555	0.719	0.0000300	6681
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0.00021	0.00020	rare
East Asian	0	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.000063	0.000062	rare
South Asian	0.000038	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.132

Intolerance Scores

LoFtool: 0.407
RVIS EVS: -0.55
RVIS percentile EVS: 19.86

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.838

Gene Damage Prediction

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