JADE3

Summary

JADE3 (jade family PHD finger 3, HGNC:22982) is a protein-coding gene on chromosome Xp11.3, encoding Protein Jade-3 (Q92613). Scaffold subunit of some HBO1 complexes, which have a histone H4 acetyltransferase activity.

This gene encodes a member of a family of large proteins containing PHD (plant homeo domain)-type zinc fingers. The encoded protein may be associated in a nuclear complex that functions in histone H4 acetylation. Alternative splicing results in multiple transcript variants encoding the same protein.

Source: NCBI Gene 9767 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 73 total — 1 pathogenic
• MANE Select transcript: NM_014735

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:22982
Approved symbol	JADE3
Name	jade family PHD finger 3
Location	Xp11.3
Locus type	gene with protein product
Status	Approved
Aliases	KIAA0215, JADE-3
Ensembl gene	ENSG00000102221
Ensembl biotype	protein_coding
OMIM	300618
Entrez	9767

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000424392, ENST00000455411, ENST00000611250, ENST00000614628

RefSeq mRNA: 2 — MANE Select: NM_014735 NM_001077445, NM_014735

CCDS: CCDS14271

Canonical transcript exons

ENST00000614628 — 11 exons

Exon	Start	End
ENSE00000669247	46998120	46998277
ENSE00000870090	46985713	46985792
ENSE00001138472	46984884	46984940
ENSE00002148804	47024724	47024914
ENSE00003718352	47038949	47039065
ENSE00003718962	47027892	47028103
ENSE00003719386	47056082	47056199
ENSE00003740726	47033621	47033788
ENSE00003744220	47054158	47054628
ENSE00003749953	47058167	47061242
ENSE00003751583	46912421	46912719

Expression profiles

Bgee: expression breadth ubiquitous, 233 present calls, max score 91.67.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 6.0079 / max 62.4054, expressed in 1522 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196143	3.1938	1364
196145	1.1852	483
196142	1.0719	565
196144	0.5570	308

Top tissues by expression

272 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
corpus epididymis	UBERON:0004359	91.67	gold quality
caput epididymis	UBERON:0004358	88.77	gold quality
placenta	UBERON:0001987	85.83	gold quality
right adrenal gland cortex	UBERON:0035827	84.01	gold quality
seminal vesicle	UBERON:0000998	83.98	gold quality
right adrenal gland	UBERON:0001233	83.44	gold quality
ganglionic eminence	UBERON:0004023	83.36	gold quality
secondary oocyte	CL:0000655	82.98	gold quality
left adrenal gland	UBERON:0001234	82.59	gold quality
adrenal gland	UBERON:0002369	82.41	gold quality
adrenal cortex	UBERON:0001235	82.36	gold quality
esophagus squamous epithelium	UBERON:0006920	82.33	gold quality
left adrenal gland cortex	UBERON:0035825	82.00	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	81.95	gold quality
cortical plate	UBERON:0005343	81.23	gold quality
embryo	UBERON:0000922	81.17	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.61	gold quality
body of pancreas	UBERON:0001150	79.56	gold quality
adrenal tissue	UBERON:0018303	79.52	gold quality
buccal mucosa cell	CL:0002336	79.40	silver quality
visceral pleura	UBERON:0002401	79.30	gold quality
gingival epithelium	UBERON:0001949	78.80	gold quality
pancreas	UBERON:0001264	78.72	gold quality
germinal epithelium of ovary	UBERON:0001304	78.31	gold quality
ventricular zone	UBERON:0003053	77.82	gold quality
islet of Langerhans	UBERON:0000006	77.77	gold quality
epithelium of esophagus	UBERON:0001976	77.72	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	77.39	gold quality
cauda epididymis	UBERON:0004360	77.04	gold quality
epithelium of nasopharynx	UBERON:0001951	77.02	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.20

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

124 targeting JADE3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-450A-1-3P	100.00	69.33	1837
HSA-MIR-3646	100.00	73.56	5283
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-30A-5P	100.00	76.31	3233
HSA-MIR-30B-5P	100.00	76.29	3248
HSA-MIR-30C-5P	100.00	76.29	3248
HSA-MIR-30D-5P	100.00	76.32	3233
HSA-MIR-30E-5P	100.00	76.32	3242
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-6870-5P	99.99	68.55	2115
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-4723-5P	99.97	68.70	2034
HSA-MIR-5698	99.97	68.49	2029
HSA-MIR-7111-5P	99.97	68.48	2062
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-23A-3P	99.95	74.24	3163

Literature-anchored findings (GeneRIF, showing 2)

• JADE3 was markedly upregulated in colon cancer tissues and correlated with cancer progression and predicted shorter patient survival. JADE3 interacted with the promoters of LGR5 and activated its transcription, by increasing the occupancy of p300 acetyltransferase and histone acetylation on the promoters. These findings suggest an oncogenic role of JADE3 by regulating cancer stem cell-like traits in the colon cancer. (PMID:29660380)
• Genome-wide CRISPR activation screen identifies JADE3 as an antiviral activator of NF-kB-dependent IFITM3 expression. (PMID:38462163)

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
danio_rerio	jade3	ENSDARG00000019614
mus_musculus	Jade3	ENSMUSG00000037315
rattus_norvegicus	Jade3	ENSRNOG00000039837
drosophila_melanogaster	rno	FBGN0035106
caenorhabditis_elegans		WBGENE00021810

Paralogs (8): JADE2 (ENSG00000043143), JADE1 (ENSG00000077684), MLLT10 (ENSG00000078403), BRPF3 (ENSG00000096070), BRD1 (ENSG00000100425), PHF14 (ENSG00000106443), BRPF1 (ENSG00000156983), MLLT6 (ENSG00000275023)

Protein

Protein identifiers

Protein Jade-3 — Q92613 (reviewed: Q92613)

Alternative names: Jade family PHD finger protein 3, PHD finger protein 16

All UniProt accessions (3): Q92613, F2Z2B6, F2Z3N8

UniProt curated annotations — full annotation on UniProt →

Function. Scaffold subunit of some HBO1 complexes, which have a histone H4 acetyltransferase activity.

Subunit / interactions. Component of the HBO1 complex composed at least of ING4 or ING5, KAT7/HBO1, MEAF6, and one of JADE1, JADE2 and JADE3.

Tissue specificity. Ubiquitously expressed, with highest levels in placenta and uterus.

Induction. By estradiol in estrogen-responsive breast cancer cells.

Similarity. Belongs to the JADE family.

RefSeq proteins (2): NP_001070913, NP_055550* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001965	Znf_PHD	Domain
IPR011011	Znf_FYVE_PHD	Homologous_superfamily
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR019542	Enhancer_polycomb-like_N	Domain
IPR019786	Zinc_finger_PHD-type_CS	Conserved_site
IPR019787	Znf_PHD-finger	Domain
IPR034732	EPHD	Domain
IPR039550	JADE3_PHD	Domain
IPR050701	Histone_Mod_Regulator	Family

Pfam: PF10513, PF13831, PF13832

UniProt features (26 total): modified residue 11, region of interest 6, compositionally biased region 5, zinc finger region 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q92613-F1	60.45	0.27

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (11): 30, 32, 85, 566, 601, 608, 638, 735, 774, 776, 780

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

ID	Pathway
R-HSA-3214847	HATs acetylate histones
R-HSA-3247509	Chromatin modifying enzymes
R-HSA-4839726	Chromatin organization

MSigDB gene sets: 208 (showing top): RNGTGGGC_UNKNOWN, MORF_MSH3, MORF_BRCA1, GOBP_GROWTH, GGGTGGRR_PAX4_03, SHIPP_DLBCL_CURED_VS_FATAL_DN, MORF_RAD51L3, TTGCWCAAY_CEBPB_02, WEI_MYCN_TARGETS_WITH_E_BOX, YOKOE_CANCER_TESTIS_ANTIGENS, CEBP_Q2, MORF_CTSB, GOBP_REGULATION_OF_CELL_CYCLE, MORF_IL4, MORF_PRKCA

GO Biological Process (6): regulation of cell growth (GO:0001558), regulation of DNA replication (GO:0006275), regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), regulation of cell cycle (GO:0051726), regulation of DNA biosynthetic process (GO:2000278)

GO Molecular Function (3): zinc ion binding (GO:0008270), protein binding (GO:0005515), metal ion binding (GO:0046872)

GO Cellular Component (2): histone acetyltransferase complex (GO:0000123), nucleoplasm (GO:0005654)

Reactome top-level categories

Rollup of top-2 pathways:

Category	Pathways
Chromatin modifying enzymes	1
Chromatin organization	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
regulation of DNA metabolic process	2
cell growth	1
regulation of growth	1
regulation of cellular component organization	1
DNA replication	1
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
regulation of DNA-templated transcription	1
transcription by RNA polymerase II	1
cell cycle	1
regulation of cellular process	1
regulation of macromolecule biosynthetic process	1
DNA biosynthetic process	1
transition metal ion binding	1
binding	1
cation binding	1
chromatin	1
protein acetyltransferase complex	1
nuclear lumen	1
cellular anatomical structure	1

Protein interactions and networks

STRING

552 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
JADE3	MEAF6	Q9HAF1	697
JADE3	KAT7	O95251	683
JADE3	ING4	Q9UNL4	678
JADE3	ASXL2	Q76L83	552
JADE3	BIN3	Q9NQY0	508
JADE3	BRPF3	Q9ULD4	486
JADE3	JADE2	Q9NQC1	470
JADE3	JADE1	Q6IE81	460
JADE3	DACT2	Q5SW24	450
JADE3	OR1L3	Q8NH93	435
JADE3	PHF12	Q96QT6	424
JADE3	BRD1	O95696	415
JADE3	DNM2	P50570	385
JADE3	ING5	Q8WYH8	384
JADE3	HMG20B	Q9P0W2	381

IntAct

63 interactions, top by confidence:

A	B	Type	Score
KAT7	JADE1	psi-mi:“MI:0914”(association)	0.720
MAGEA11	JADE3	psi-mi:“MI:0915”(physical association)	0.680
JADE3	MAGEA11	psi-mi:“MI:0915”(physical association)	0.560
MAGEA11	JADE3	psi-mi:“MI:0915”(physical association)	0.560
CASP6	JADE3	psi-mi:“MI:0915”(physical association)	0.560
DR1	JADE3	psi-mi:“MI:0915”(physical association)	0.560
JADE3	GFAP	psi-mi:“MI:0915”(physical association)	0.560
GTF2B	JADE3	psi-mi:“MI:0915”(physical association)	0.560
LAMP2	JADE3	psi-mi:“MI:0915”(physical association)	0.560
JADE3	NDUFV2	psi-mi:“MI:0915”(physical association)	0.560
TARDBP	JADE3	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (71): JADE3 (Two-hybrid), JADE3 (Proximity Label-MS), JADE3 (Affinity Capture-MS), JADE3 (Affinity Capture-MS), JADE3 (Affinity Capture-MS), JADE3 (Affinity Capture-MS), JADE3 (Affinity Capture-MS), JADE3 (Affinity Capture-MS), JADE3 (Affinity Capture-MS), JADE3 (Affinity Capture-MS), JADE3 (Affinity Capture-MS), JADE3 (Affinity Capture-MS), JADE3 (Co-localization), JADE3 (Protein-RNA), JADE3 (Two-hybrid)

ESM2 similar proteins: A0A1P8AW69, A1A4L4, A2RRS8, A2RVA7, B3H5K9, B8QB46, F4HTH8, F4KB17, P62285, P62287, P62288, P62289, P62290, P62291, P62292, P62293, P62294, P62297, Q08AX9, Q08DB0, Q0P4S5, Q0VA42, Q3B7T8, Q3UQI9, Q4R7I0, Q5HZK1, Q5JTW2, Q5ZIX8, Q6DJS0, Q6IE81, Q6IFT4, Q6ING4, Q6IRU7, Q6NPP4, Q6REY9, Q6ZEZ5, Q75PQ8, Q7ZXG4, Q8AYG3, Q8CJ27

Diamond homologs: A0A286Y9D1, A1YVX4, A7E320, B2KF05, B2RRD7, B6CHA3, F4KBP5, F6UA42, G5E8P1, G5EBZ4, O54826, O75164, O94880, O94953, P0CB22, P29375, P34447, P41229, P41230, P47156, P55197, P55198, P55201, Q0P4S5, Q12311, Q20318, Q22516, Q29EQ3, Q30DN6, Q38JA7, Q3UXZ9, Q5E9T7, Q5RD88, Q5TKR9, Q62240, Q6GQJ2, Q6IE81, Q6IE82, Q6IQX0, Q6K431

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 50 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
HATs acetylate histones	11	24.2×	1e-10
Chromatin organization	7	15.9×	3e-05
Chromatin modifying enzymes	7	14.1×	4e-05
Transcriptional Regulation by TP53	5	8.6×	7e-03

GO biological processes:

GO term	Partners	Fold	FDR
regulation of DNA replication	5	40.7×	9e-06
regulation of cell growth	6	29.6×	4e-06
regulation of cell cycle	9	14.9×	1e-06
regulation of apoptotic process	5	9.3×	5e-03
chromatin remodeling	5	8.1×	8e-03
positive regulation of apoptotic process	6	7.6×	4e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

73 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	65
Likely benign	7
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
831193	NC_000023.10:g.(?46719423)(46952346_?)del	Pathogenic

SpliceAI

2258 predictions. Top by Δscore:

Variant	Effect	Δscore
X:46984880:CCA:C	acceptor_loss	1.0000
X:46984881:CAGG:C	acceptor_loss	1.0000
X:46984882:A:AC	acceptor_loss	1.0000
X:46984882:A:AG	acceptor_gain	1.0000
X:46984882:AG:A	acceptor_gain	1.0000
X:46984883:G:GC	acceptor_loss	1.0000
X:46984883:G:GG	acceptor_gain	1.0000
X:46984883:GG:G	acceptor_gain	1.0000
X:46984883:GGA:G	acceptor_gain	1.0000
X:46984883:GGAT:G	acceptor_gain	1.0000
X:46984936:CGAAA:C	donor_gain	1.0000
X:46984937:GAAA:G	donor_gain	1.0000
X:46984937:GAAAG:G	donor_gain	1.0000
X:46984939:AAGTG:A	donor_loss	1.0000
X:46984941:G:GG	donor_gain	1.0000
X:46984943:GAG:G	donor_loss	1.0000
X:46984944:A:AC	donor_loss	1.0000
X:46985708:CACA:C	acceptor_loss	1.0000
X:46985710:CAGGT:C	acceptor_loss	1.0000
X:46985711:A:AG	acceptor_gain	1.0000
X:46985711:A:AT	acceptor_loss	1.0000
X:46985712:G:GC	acceptor_loss	1.0000
X:46985712:G:GG	acceptor_gain	1.0000
X:46985788:CTGAG:C	donor_loss	1.0000
X:46985790:GAGGT:G	donor_loss	1.0000
X:46985791:AGGT:A	donor_loss	1.0000
X:46985794:T:G	donor_loss	1.0000
X:46998277:GGTA:G	donor_loss	1.0000
X:46998278:G:T	donor_loss	1.0000
X:47024713:T:TA	acceptor_gain	1.0000

AlphaMissense

5520 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:47028023:T:A	C203S	1.000
X:47028023:T:C	C203R	1.000
X:47028024:G:A	C203Y	1.000
X:47028024:G:C	C203S	1.000
X:47028025:T:G	C203W	1.000
X:47028032:T:A	C206S	1.000
X:47028032:T:C	C206R	1.000
X:47028033:G:C	C206S	1.000
X:47028071:T:C	F219L	1.000
X:47028073:C:A	F219L	1.000
X:47028073:C:G	F219L	1.000
X:47028074:T:C	C220R	1.000
X:47028075:G:A	C220Y	1.000
X:47028076:T:G	C220W	1.000
X:47028098:C:A	H228N	1.000
X:47028098:C:G	H228D	1.000
X:47028100:T:A	H228Q	1.000
X:47028100:T:G	H228Q	1.000
X:47033624:T:C	C231R	1.000
X:47033625:G:A	C231Y	1.000
X:47033626:C:G	C231W	1.000
X:47033657:T:A	W242R	1.000
X:47033657:T:C	W242R	1.000
X:47033663:T:C	C244R	1.000
X:47033696:T:C	C255R	1.000
X:47033698:T:G	C255W	1.000
X:47033705:T:C	C258R	1.000
X:47033768:T:C	C279R	1.000
X:47033770:T:G	C279W	1.000
X:47033777:T:A	W282R	1.000

dbSNP variants (sampled 300 via entrez): RS1000004661 (X:46934456 G>A), RS1000008219 (X:46975058 G>T), RS1000054742 (X:46985108 A>C), RS1000097859 (X:46955555 A>G), RS1000211679 (X:46926972 C>T), RS1000265984 (X:47052513 A>T), RS1000275090 (X:46984548 T>C), RS1000313480 (X:46915699 A>T), RS1000325839 (X:46926512 C>T), RS1000358031 (X:47031811 G>A), RS1000434453 (X:46994643 A>G), RS1000469621 (X:47053009 T>C), RS1000528038 (X:46975526 T>G), RS1000558678 (X:47004658 C>T), RS1000618235 (X:46995137 C>T)

Disease associations

OMIM: gene MIM:300618 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases methylation	4
bisphenol A	increases expression, increases methylation	2
sodium arsenite	affects methylation, increases abundance, increases expression	2
Air Pollutants	decreases expression, increases abundance	2
Particulate Matter	decreases expression, increases abundance, decreases reaction, increases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
beta-lapachone	increases expression	1
arsenite	affects binding, decreases reaction	1
coumarin	decreases phosphorylation	1
di-n-butylphosphoric acid	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
2-methyl-2H-pyrazole-3-carboxylic acid (2-methyl-4-o-tolylazophenyl)amide	decreases reaction, increases expression	1
Sunitinib	increases expression	1
Acetaminophen	increases expression	1
Arsenic	increases abundance, increases expression	1
Vehicle Emissions	decreases reaction, increases expression	1
Benzo(a)pyrene	affects methylation	1
Caffeine	affects phosphorylation	1
Coal	decreases expression, increases abundance	1
Hydrogen Peroxide	decreases expression	1
Lead	affects expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression, increases abundance	1
Tobacco Smoke Pollution	increases methylation	1
Tretinoin	decreases expression	1
Cyclosporine	increases expression	1
Aflatoxin B1	decreases methylation	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.