JADE1

protein-coding

jade family PHD finger 1, the group of PHD finger proteins

Gene summary

Enables transcription coactivator activity. Contributes to histone acetyltransferase activity. Involved in several processes, including negative regulation of canonical Wnt signaling pathway; regulation of DNA metabolic process; and regulation of cell growth. Acts upstream of or within negative regulation of G1/S transition of mitotic cell cycle. Located in several cellular components, including ciliary basal body; cytosol; and nuclear speck. Part of histone acetyltransferase complex. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

PHF17

MANE transcript

NM_199320.4

Inheritance

—

ClinVar variants

U:75B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.11

Max pathogenic AF

—

Genomic locus

chr4:128,809,700-128,875,224

External References & Databases

Ensembl (ENSG00000077684)

Transcript & Mutation Effects

hg38 • Region Span ~65.5 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 JADE1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 75

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_199320.4. 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	2
missense			75 clinvar		1 clinvar	76
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	75	0	3	78

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 122 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_199320.4	RefSeq	NP_955352.1	10	MANE Select
ENST00000226319.11	Ensembl	ENSP00000226319.6	10	MANE Select
NM_001287437.2	RefSeq	NP_001274366.1	10	Standard
NM_001287439.2	RefSeq	NP_001274368.1	10	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
jade1	Danio rerio	Structure: whole organism Quality: increased curvature abnormal

Gene / Model

Organism

Observed Phenotype

jade1

Danio rerio

Structure: whole organism

Quality: increased curvature

abnormal

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

apoptotic process
negative regulation of cell growth
histone H3 acetylation
histone H4-K5 acetylation
histone H4-K8 acetylation

Molecular Function

transcription coactivator activity
protein binding
metal ion binding

Cellular Component

histone acetyltransferase complex
nucleus
nucleoplasm
cytoplasm
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000226319
Coding exons: 10
Length: 65601
Individuals with no LoFs: 125735
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125744
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.18	281	476	0.590	0.0000264	5566
Missense (PolyPhen)		27	135.04	0.19995		1501
Synonymous	1.03	167	185	0.903	0.0000100	1606
Loss of Function	5.05	4	37.3	0.107	0.00000201	442

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000070	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. Transcriptional coactivator, it may also promote acetylation of nucleosomal histone H4 by KAT5. Promotes apoptosis. May act as a renal tumor suppressor. Negatively regulates canonical Wnt signaling; at least in part, cooperates with NPHP4 in this function. {ECO:0000269|PubMed:15502158, ECO:0000269|PubMed:16046545, ECO:0000269|PubMed:16387653, ECO:0000269|PubMed:22654112}.;

Recessive Scores

pRec: 0.127

Intolerance Scores

RVIS EVS: -0.51
RVIS percentile EVS: 21.73

Essentials

Essential (gene trap): N

Gene Damage Prediction

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