JADE2

protein-coding

jade family PHD finger 2, the group of PHD finger proteins

Gene summary

Enables histone H4K12 acetyltransferase activity; histone H4K5 acetyltransferase activity; and histone H4K8 acetyltransferase activity. Contributes to histone H3K14 acetyltransferase activity. Involved in regulation of DNA biosynthetic process; regulation of DNA replication; and regulation of cell cycle. Located in nucleoplasm. Part of histone acetyltransferase complex. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

PHF15

MANE transcript

NM_001388185.1

Inheritance

—

ClinVar variants

U:96B:6

Top phenotype

JADE2-associated Neurodevelopmental Disorder

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr5:134,524,312-134,583,230

External References & Databases

Ensembl (ENSG00000043143)

Transcript & Mutation Effects

hg38 • Region Span ~58.9 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 JADE2 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 99

not providedTotal: 2

JADE2-associated Neurodevelopmental DisorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001388185.1. 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				1 clinvar		1
missense			95 clinvar	3 clinvar	2 clinvar	100
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	96	4	2	102

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 100 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001388185.1	RefSeq	NP_001375114.1	11	MANE Select
ENST00000681547.2	Ensembl	ENSP00000505514.1	11	MANE Select
NM_001289984.2	RefSeq	NP_001276913.1	10	Standard
NM_001289985.2	RefSeq	NP_001276914.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Chromatin modifying enzymes
HATs acetylate histones
Chromatin organization

Biological Process

protein ubiquitination
histone H3 acetylation
histone H4-K5 acetylation
histone H4-K8 acetylation
histone H4-K12 acetylation

Molecular Function

protein binding
transferase activity
metal ion binding

Cellular Component

histone acetyltransferase complex
nucleoplasm
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000395003
Coding exons: 10
Length: 58916
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125747
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.46	347	502	0.691	0.0000320	5109
Missense (PolyPhen)		107	217.46	0.49205		2374
Synonymous	-0.113	216	214	1.01	0.0000150	1615
Loss of Function	5.26	2	36.2	0.0553	0.00000207	373

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00016	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000035	0.000026	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Component of the HBO1 complex which has a histone H4- specific acetyltransferase activity, a reduced activity toward histone H3 and is responsible for the bulk of histone H4 acetylation in vivo (PubMed:16387653). Acts as a E3 ubiquitin- protein ligase mediating the ubiquitination and subsequent proteasomal degradation of target protein histone demethylase KDM1A (PubMed:25018020). Also acts as a ubiquitin ligase E3 toward itself. Positive regulator of neurogenesis (By similarity). {ECO:0000250|UniProtKB:Q6ZQF7, ECO:0000269|PubMed:16387653}.;

Recessive Scores

pRec: 0.109

Intolerance Scores

RVIS EVS: -0.48
RVIS percentile EVS: 22.75

Essentials

Essential (gene trap): N

Gene Damage Prediction

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