PHF20L1

protein-coding

PHD finger protein 20 like 1, the group of Tudor domain containing|PHD finger proteins

Gene summary

Enables methylation-dependent protein binding activity. Involved in negative regulation of proteasomal ubiquitin-dependent protein catabolic process. Predicted to be located in nucleoplasm. Predicted to be part of NSL complex. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_016018.5

Inheritance

—

ClinVar variants

U:98B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.09

Max pathogenic AF

—

Genomic locus

chr8:132,775,358-132,848,807

External References & Databases

Ensembl (ENSG00000129292)

Transcript & Mutation Effects

hg38 • Region Span ~73.4 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 PHF20L1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 89

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016018.5. 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		1 clinvar	3
missense			88 clinvar	2 clinvar		90
nonsense			1 clinvar			1
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	98	2	1	101

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 124 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016018.5	RefSeq	NP_057102.4	20	MANE Select
ENST00000395386.7	Ensembl	ENSP00000378784.2	20	MANE Select
NM_001277196.2	RefSeq	NP_001264125.1	19	Standard
NM_001362971.2	RefSeq	NP_001349900.1	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of transcription, DNA-templated

Molecular Function

protein binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000395386
Coding exons: 20
Length: 73435
Individuals with no LoFs: 125727
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125736
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.85	418	538	0.776	0.0000278	6726
Missense (PolyPhen)		109	194.08	0.56162		2423
Synonymous	-0.0969	185	183	1.01	0.00000962	1830
Loss of Function	6.33	5	56.3	0.0889	0.00000310	694

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000036	0.000035	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.103

Intolerance Scores

LoFtool: 0.476
RVIS EVS: -1.37
RVIS percentile EVS: 4.43

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.588

Gene Damage Prediction

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