JADE1

Summary

JADE1 (jade family PHD finger 1, HGNC:30027) is a protein-coding gene on chromosome 4q28.2, encoding Protein Jade-1 (Q6IE81). Scaffold subunit of some HBO1 complexes, which have a histone H4 acetyltransferase activity.

Enables transcription coactivator activity. Contributes to histone acetyltransferase activity. Involved in several processes, including negative regulation of canonical Wnt signaling pathway; regulation of cell growth; and regulation of nucleobase-containing compound metabolic process. Acts upstream of or within negative regulation of G1/S transition of mitotic cell cycle. Located in several cellular components, including cytosol; microtubule organizing center; and nuclear speck. Part of histone acetyltransferase complex.

Source: NCBI Gene 79960 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 82 total
• MANE Select transcript: NM_199320

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30027
Approved symbol	JADE1
Name	jade family PHD finger 1
Location	4q28.2
Locus type	gene with protein product
Status	Approved
Aliases	JADE-1
Ensembl gene	ENSG00000077684
Ensembl biotype	protein_coding
OMIM	610514
Entrez	79960

Gene structure

Transcript identifiers

Ensembl transcripts: 45 — 44 protein_coding, 1 nonsense_mediated_decay

ENST00000226319, ENST00000413543, ENST00000452328, ENST00000503785, ENST00000504089, ENST00000507833, ENST00000508997, ENST00000510308, ENST00000511647, ENST00000511925, ENST00000512960, ENST00000514740, ENST00000610919, ENST00000611140, ENST00000887594, ENST00000887595, ENST00000887596, ENST00000887597, ENST00000887598, ENST00000887599, ENST00000887600, ENST00000887601, ENST00000887602, ENST00000887603, ENST00000887604, ENST00000887605, ENST00000887606, ENST00000933989, ENST00000933990, ENST00000933991, ENST00000933992, ENST00000933993, ENST00000933994, ENST00000933995, ENST00000933996, ENST00000933997, ENST00000933998, ENST00000933999, ENST00000947587, ENST00000947588, ENST00000947589, ENST00000947590, ENST00000947591, ENST00000947592, ENST00000947593

RefSeq mRNA: 8 — MANE Select: NM_199320 NM_001287437, NM_001287439, NM_001287440, NM_001287441, NM_001287442, NM_001287443, NM_024900, NM_199320

CCDS: CCDS34062, CCDS47134, CCDS75191

Canonical transcript exons

ENST00000226319 — 11 exons

Exon	Start	End
ENSE00001517906	128809700	128809877
ENSE00003889275	128871355	128875224
ENSE00003889294	128867856	128867973
ENSE00003890361	128852057	128852268
ENSE00003891670	128842953	128843038
ENSE00003891680	128831733	128831810
ENSE00003891995	128846375	128846532
ENSE00003893121	128855630	128855797
ENSE00003894005	128861704	128862225
ENSE00003895714	128848980	128849167
ENSE00003895981	128857338	128857454

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 95.57.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 16.8492 / max 150.0290, expressed in 1758 samples.

FANTOM5 promoters (9 alternative TSS)

Promoter ID	TPM avg	Samples expressed
49638	9.9950	1692
49639	2.3882	1317
49643	2.0290	1025
49644	0.7945	414
49641	0.5468	262
49637	0.3696	189
49645	0.3573	183
49640	0.2734	134
49642	0.0954	50

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	95.57	gold quality
pericardium	UBERON:0002407	95.03	gold quality
parotid gland	UBERON:0001831	94.97	gold quality
ventricular zone	UBERON:0003053	94.70	gold quality
nephron tubule	UBERON:0001231	94.64	gold quality
body of pancreas	UBERON:0001150	93.58	gold quality
renal glomerulus	UBERON:0000074	93.48	gold quality
kidney epithelium	UBERON:0004819	93.42	gold quality
mucosa of stomach	UBERON:0001199	93.37	gold quality
metanephric glomerulus	UBERON:0004736	92.95	gold quality
calcaneal tendon	UBERON:0003701	92.85	gold quality
tibia	UBERON:0000979	92.82	gold quality
pancreas	UBERON:0001264	92.51	gold quality
middle temporal gyrus	UBERON:0002771	92.49	gold quality
lower lobe of lung	UBERON:0008949	92.21	gold quality
tendon	UBERON:0000043	91.51	gold quality
left coronary artery	UBERON:0001626	91.41	gold quality
coronary artery	UBERON:0001621	91.26	gold quality
adrenal tissue	UBERON:0018303	91.05	gold quality
cortex of kidney	UBERON:0001225	90.97	gold quality
right lobe of thyroid gland	UBERON:0001119	90.89	gold quality
mucosa of paranasal sinus	UBERON:0005030	90.82	gold quality
islet of Langerhans	UBERON:0000006	90.79	gold quality
kidney	UBERON:0002113	90.78	gold quality
thyroid gland	UBERON:0002046	90.63	gold quality
metanephros	UBERON:0000081	90.58	gold quality
left lobe of thyroid gland	UBERON:0001120	90.57	gold quality
ganglionic eminence	UBERON:0004023	90.57	gold quality
dorsal motor nucleus of vagus nerve	UBERON:0002870	90.32	gold quality
adult mammalian kidney	UBERON:0000082	90.29	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	13.37
E-MTAB-6058	no	241.07

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): POU5F1

miRNA regulators (miRDB)

109 targeting JADE1, 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-8485	100.00	77.57	4731
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-1252-5P	100.00	69.80	2774
HSA-MIR-4673	100.00	66.64	1490
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-4645-5P	99.98	65.81	1284
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-1250-3P	99.96	70.04	4038
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-548AB	99.95	71.31	3488
HSA-LET-7C-3P	99.95	73.42	2862
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509

Literature-anchored findings (GeneRIF, showing 19)

• Jade-1 protein is a novel candidate regulatory factor in Von Hippel Lindau-mediated renal tumor suppression (PMID:12169691)
• Jade-1 is a novel candidate transcriptional co-activator associated with HAT activity and may play a key role in the pathogenesis of renal cancer and von Hippel-Lindau disease (PMID:15502158)
• Jade-1 may suppress renal cancer cell growth in part by increasing apoptosis. (PMID:16046545)
• Jade-1/1L are crucial co-factors for HBO1-mediated histone H4 acetylation (PMID:18684714)
• The pVHL tumour suppressor and the Wnt tumorigenesis pathway are therefore directly linked through Jade-1. (PMID:18806787)
• RCC with a low expression of Jade-1 is associated with a poor outcome and decreased survival (PMID:22516360)
• The ciliary protein nephrocystin-4 translocates the canonical Wnt regulator Jade-1 to the nucleus to negatively regulate beta-catenin signaling. (PMID:22654112)
• Reduced Jade-1 expression is associated with clear-cell renal cell carcinomas. (PMID:23824745)
• lncRNA-JADE is a key functional link that connects the DDR to histone H4 acetylation, and that dysregulation of lncRNA-JADE may contribute to breast tumorigenesis. (PMID:24097061)
• Increase in the number of cells with cytoplasmic JADE1S correlated with activation of tubular cell proliferation and inversely correlated with the number of cells with nuclear JADE1S, supporting role of HBO1-JADE1 shuttling during organ regeneration. (PMID:24739512)
• Casein kinase 1 alpha specifically phosphorylates Jade-1 at an unprimed SLS phosphorylation site. (PMID:25100726)
• JADE1S protein localized to centrosomes in interphase and mitotic cells, and to the midbody during cytokinesis. (PMID:26151225)
• Interactome analyses revealed that the Jade-1S mutant unable to be phosphorylated by CK1alpha has an increased binding affinity to proteins involved in chromatin remodelling, histone deacetylation, transcriptional repression, and ribosome biogenesis. (PMID:26919559)
• JADE1 expression has a role in colon cancers, renal carcinomas, and in acute kidney injuries and regeneration. (Review) (PMID:27155521)
• identification of SNPs within the IQCJ, NXPH1, PHF17 and MYB genes partly explaining the large interindividual variability observed in plasma triglyceride levels in response to an n-3 fatty acid supplementation (PMID:27160456)
• A genome-wide association study (GWAS) identified loci associated with the plasma triglyceride (TG) response to omega-3 fatty acid (FA) supplementation in IQCJ, NXPH1, PHF17 and MYB. (PMID:28134766)
• results indicate that the N-terminal region of JADE1 functions as a platform that brings together the catalytic HBO1 subunit with its cognate H3-H4 substrate for histone acetylation (PMID:29382722)
• Genome-wide association study and functional validation implicates JADE1 in tauopathy. (PMID:34719765)
• MicroRNA-155-5p Targets JADE-1, Promoting Proliferation, Migration, and Invasion in Clear Cell Renal Cell Carcinoma Cells. (PMID:37175531)

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
danio_rerio	jade1	ENSDARG00000033707
mus_musculus	Jade1	ENSMUSG00000025764
rattus_norvegicus	Jade1	ENSRNOG00000014066
drosophila_melanogaster	Alh	FBGN0261238
caenorhabditis_elegans		WBGENE00006975
caenorhabditis_elegans		WBGENE00021810

Paralogs (8): JADE2 (ENSG00000043143), MLLT10 (ENSG00000078403), BRPF3 (ENSG00000096070), BRD1 (ENSG00000100425), JADE3 (ENSG00000102221), PHF14 (ENSG00000106443), BRPF1 (ENSG00000156983), MLLT6 (ENSG00000275023)

Protein

Protein identifiers

Protein Jade-1 — Q6IE81 (reviewed: Q6IE81)

Alternative names: Jade family PHD finger protein 1, PHD finger protein 17

All UniProt accessions (8): Q6IE81, D6RAS5, D6RBB3, D6RC05, D6RCS1, D6RE74, D6RFK0, D6RGE7

UniProt curated annotations — full annotation on UniProt →

Function. Scaffold subunit of some HBO1 complexes, which have a histone H4 acetyltransferase activity. Plays a key role in HBO1 complex by directing KAT7/HBO1 specificity towards histone H4 acetylation (H4K5ac, H4K8ac and H4K12ac), regulating DNA replication initiation, regulating DNA replication initiation. 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.

Subunit / interactions. Component of the HBO1 complex composed at least of ING4 or ING5, KAT7/HBO1, MEAF6, and one of JADE1, JADE2 and JADE3. Interacts with NPHP4. Interacts with VHL and KAT5. Does not associate with ING4 or ING5, and does not act as a component of the HBO1 complex.

Subcellular location. Nucleus. Chromosome. Cytoplasm. Cytoskeleton. Cilium basal body.

Tissue specificity. Highly expressed in kidney. Also present in pancreas, liver and heart (at protein level). Down-regulated in renal cancer cells.

Domain organisation. The 2 PHD-type zinc fingers are required for transcriptional activity.

Similarity. Belongs to the JADE family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6IE81-1	1, JADE1L	yes
Q6IE81-2	2
Q6IE81-3	3, JADE1S

RefSeq proteins (8): NP_001274366, NP_001274368, NP_001274369, NP_001274370, NP_001274371, NP_001274372, NP_079176, NP_955352* (*=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
IPR039546	Jade-1_PHD	Domain
IPR050701	Histone_Mod_Regulator	Family

Pfam: PF10513, PF13831, PF13832

UniProt features (44 total): strand 9, region of interest 7, helix 7, modified residue 6, turn 4, zinc finger region 3, splice variant 3, cross-link 2, chain 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
8GE0	X-RAY DIFFRACTION	2.4
8GDX	X-RAY DIFFRACTION	2.74

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6IE81-F1	62.34	0.25

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 (8): 89, 92, 603, 609, 703, 743, 114, 573

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: 443 (showing top): RNGTGGGC_UNKNOWN, E2F_Q4, E2F_Q4_01, BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_DN, BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, HNF3ALPHA_Q6, E2F4DP1_01, GCANCTGNY_MYOD_Q6, GOBP_NEGATIVE_REGULATION_OF_CELL_GROWTH, GOBP_CELL_CYCLE_PHASE_TRANSITION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP, GOBP_GROWTH, TAL1ALPHAE47_01, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY

GO Biological Process (12): regulation of cell growth (GO:0001558), regulation of DNA replication (GO:0006275), chromatin remodeling (GO:0006338), regulation of DNA-templated transcription (GO:0006355), regulation of transcription by RNA polymerase II (GO:0006357), apoptotic process (GO:0006915), negative regulation of cell growth (GO:0030308), regulation of cell cycle (GO:0051726), negative regulation of canonical Wnt signaling pathway (GO:0090090), negative regulation of G1/S transition of mitotic cell cycle (GO:2000134), regulation of DNA biosynthetic process (GO:2000278), positive regulation of DNA-templated transcription (GO:0045893)

GO Molecular Function (8): transcription coactivator activity (GO:0003713), zinc ion binding (GO:0008270), protein binding (GO:0005515), histone H3K14 acetyltransferase activity (GO:0036408), histone H4K5 acetyltransferase activity (GO:0043995), histone H4K8 acetyltransferase activity (GO:0043996), histone H4K12 acetyltransferase activity (GO:0043997), metal ion binding (GO:0046872)

GO Cellular Component (12): histone acetyltransferase complex (GO:0000123), nucleus (GO:0005634), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), centrosome (GO:0005813), cytosol (GO:0005829), plasma membrane (GO:0005886), nuclear speck (GO:0016607), ciliary basal body (GO:0036064), chromosome (GO:0005694), cytoskeleton (GO:0005856), cell projection (GO:0042995)

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
cellular anatomical structure	4
histone H4 acetyltransferase activity	3
cell growth	2
regulation of DNA metabolic process	2
DNA-templated transcription	2
regulation of DNA-templated transcription	2
microtubule organizing center	2
intracellular membraneless organelle	2
regulation of growth	1
regulation of cellular component organization	1
DNA replication	1
chromatin organization	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
transcription by RNA polymerase II	1
programmed cell death	1
apoptotic signaling pathway	1
execution phase of apoptosis	1
regulation of cell growth	1
negative regulation of growth	1
negative regulation of cellular process	1
cell cycle	1
regulation of cellular process	1
negative regulation of Wnt signaling pathway	1
canonical Wnt signaling pathway	1
regulation of canonical Wnt signaling pathway	1
G1/S transition of mitotic cell cycle	1
negative regulation of mitotic cell cycle phase transition	1
negative regulation of cell cycle G1/S phase transition	1
regulation of G1/S transition of mitotic cell cycle	1
regulation of macromolecule biosynthetic process	1
DNA biosynthetic process	1
positive regulation of RNA biosynthetic process	1
transcription coregulator activity	1
positive regulation of DNA-templated transcription	1
transition metal ion binding	1
binding	1
histone H3 acetyltransferase activity	1
cation binding	1
chromatin	1

Protein interactions and networks

STRING

782 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
JADE1	ING4	Q9UNL4	985
JADE1	KAT7	O95251	982
JADE1	MEAF6	Q9HAF1	962
JADE1	ING5	Q8WYH8	913
JADE1	VHL	P40337	758
JADE1	H3-7	Q5TEC6	666
JADE1	H3-5	Q6NXT2	666
JADE1	H3C14	Q71DI3	666
JADE1	H3-4	Q16695	665
JADE1	SFMBT2	Q5VUG0	663
JADE1	NPHP4	O75161	624
JADE1	SMOC1	Q9H4F8	592
JADE1	H4C16	P02304	571
JADE1	BRPF1	P55201	567
JADE1	H4C7	Q99525	562

IntAct

36 interactions, top by confidence:

A	B	Type	Score
JADE1	KAT7	psi-mi:“MI:0915”(physical association)	0.720
JADE1	KAT7	psi-mi:“MI:0914”(association)	0.720
KAT7	JADE1	psi-mi:“MI:0914”(association)	0.720
YJU2	JADE1	psi-mi:“MI:0915”(physical association)	0.560
JADE1	YJU2	psi-mi:“MI:0915”(physical association)	0.560
JADE1	UBE3A	psi-mi:“MI:0915”(physical association)	0.550
ING4	KAT7	psi-mi:“MI:0914”(association)	0.530
ING5	KAT7	psi-mi:“MI:0914”(association)	0.530
MEAF6	ANKRD17	psi-mi:“MI:0914”(association)	0.530
JADE1	NPHP4	psi-mi:“MI:0915”(physical association)	0.460
JADE1	NPHP4	psi-mi:“MI:0403”(colocalization)	0.460
JADE1	SPTAN1	psi-mi:“MI:0915”(physical association)	0.400
JADE1	VHL	psi-mi:“MI:0915”(physical association)	0.370
CFTR	JADE1	psi-mi:“MI:0915”(physical association)	0.370
HMOX2	JADE1	psi-mi:“MI:0915”(physical association)	0.370
JADE1	PFDN1	psi-mi:“MI:0915”(physical association)	0.370
JADE1	SEPTIN8	psi-mi:“MI:0915”(physical association)	0.370
JADE1	SMN1	psi-mi:“MI:0915”(physical association)	0.370
TK1	JADE1	psi-mi:“MI:0915”(physical association)	0.370
MEAF6	DAPK3	psi-mi:“MI:0914”(association)	0.350
CSNK2B	OSBPL8	psi-mi:“MI:0914”(association)	0.350
H2BC21	SMCHD1	psi-mi:“MI:0914”(association)	0.350
SSRP1	DDX39A	psi-mi:“MI:0914”(association)	0.350
ING5	CCDC85C	psi-mi:“MI:0914”(association)	0.350
MEAF6	KPNA5	psi-mi:“MI:0914”(association)	0.350

BioGRID (174): UBE2E1 (Reconstituted Complex), UBE2H (Reconstituted Complex), JADE1 (Two-hybrid), NPHP4 (Affinity Capture-Western), JADE1 (Affinity Capture-Western), KAT7 (Affinity Capture-MS), JADE1 (Co-localization), JADE1 (Affinity Capture-Western), KAT7 (Affinity Capture-Western), JADE1 (Affinity Capture-MS), JADE1 (Affinity Capture-MS), JADE1 (Affinity Capture-MS), JADE1 (Affinity Capture-MS), JADE1 (Affinity Capture-MS), JADE1 (Two-hybrid)

ESM2 similar proteins: A0A1L8HU22, A1A5R8, A8K979, B8A5Y1, E1BB03, F6UH96, O75113, P62283, P62285, P62286, P62287, P62288, P62289, P62290, P62291, P62292, P62293, P62294, P62296, P62297, Q08AX9, Q3MHN7, Q3US16, Q5BKS4, Q5HZL1, Q5XKL5, Q5ZIX8, Q5ZLE9, Q64702, Q68FF0, Q6A037, Q6IE81, Q6NQ79, Q6NSI8, Q6NZP1, Q6PCM1, Q8BMI4, Q8BVE8, Q8BZ05, 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

4 interactions.

A	Effect	B	Mechanism
SIAH1	“down-regulates quantity by destabilization”	JADE1	polyubiquitination
PKD1	“down-regulates quantity by destabilization”	JADE1	binding
CSNK1A1	“down-regulates activity”	JADE1	phosphorylation

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 29 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	5	18.0×	1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	75
Likely benign	0
Benign	5

Top pathogenic / likely-pathogenic (0)

SpliceAI

2670 predictions. Top by Δscore:

Variant	Effect	Δscore
4:128809874:GCAG:G	donor_gain	1.0000
4:128809876:AGGTA:A	donor_loss	1.0000
4:128809878:GT:G	donor_loss	1.0000
4:128831806:TGGCA:T	donor_gain	1.0000
4:128831807:GGCA:G	donor_gain	1.0000
4:128831807:GGCAG:G	donor_gain	1.0000
4:128831808:GCA:G	donor_gain	1.0000
4:128831808:GCAG:G	donor_gain	1.0000
4:128831809:CA:C	donor_gain	1.0000
4:128831811:G:GG	donor_gain	1.0000
4:128831812:T:A	donor_loss	1.0000
4:128842949:TTAGG:T	acceptor_loss	1.0000
4:128842950:TA:T	acceptor_loss	1.0000
4:128842951:A:AC	acceptor_loss	1.0000
4:128842951:A:AG	acceptor_gain	1.0000
4:128842952:G:GA	acceptor_gain	1.0000
4:128842952:GGCCT:G	acceptor_gain	1.0000
4:128843034:CAGAG:C	donor_loss	1.0000
4:128843035:AGAGG:A	donor_loss	1.0000
4:128843036:GAG:G	donor_gain	1.0000
4:128843037:AGGT:A	donor_loss	1.0000
4:128843040:T:G	donor_loss	1.0000
4:128846435:GA:G	donor_gain	1.0000
4:128846436:A:G	donor_gain	1.0000
4:128846471:G:GT	donor_gain	1.0000
4:128846472:A:T	donor_gain	1.0000
4:128848971:A:AG	acceptor_gain	1.0000
4:128848976:CCAG:C	acceptor_loss	1.0000
4:128848978:A:AG	acceptor_gain	1.0000
4:128848978:AG:A	acceptor_gain	1.0000

AlphaMissense

0 scored. Top likely-pathogenic:

dbSNP variants (sampled 300 via entrez): RS1000048565 (4:128870311 G>C), RS1000110752 (4:128837474 G>T), RS1000133668 (4:128809333 T>C), RS1000155625 (4:128844795 C>T), RS1000174661 (4:128827152 T>C), RS1000183232 (4:128809574 C>A,G), RS1000249217 (4:128845878 T>G), RS1000301428 (4:128846153 C>CTG), RS1000403610 (4:128838660 T>A), RS1000457664 (4:128842890 C>A), RS1000488907 (4:128843144 G>T), RS1000547609 (4:128837653 T>C), RS10006958 (4:128832505 G>A), RS1000740182 (4:128858451 G>C), RS1000774857 (4:128818739 A>C,G)

Disease associations

OMIM: gene MIM:610514 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST001859_20	Thiazide-induced adverse metabolic effects in hypertensive patients	4.000000e-06
GCST006055_4	Response to long-chain n-3 polyunsaturated fatty acid supplementation (change in triglyceride levels)	1.000000e-06
GCST006143_10	Bone mineral density (total hip)	6.000000e-06
GCST008403_43	Arterial stiffness index	6.000000e-06

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0007681	triglyceride change measurement
EFO:0007702	hip bone mineral density
EFO:0004517	arterial stiffness measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

52 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	decreases expression, affects expression, increases methylation, affects cotreatment	8
trichostatin A	decreases expression, affects cotreatment	3
bisphenol A	decreases expression, affects cotreatment, increases expression	2
Benzo(a)pyrene	decreases expression	2
Dexamethasone	increases expression, affects cotreatment	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Plant Extracts	affects cotreatment, increases expression, decreases expression	2
Progesterone	increases expression	2
Tretinoin	decreases expression	2
Cadmium Chloride	decreases expression, increases abundance, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
Particulate Matter	increases expression, decreases expression, increases abundance	2
aristolochic acid I	decreases expression	1
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamide	decreases expression	1
GSK-J4	increases expression	1
afuresertib	decreases expression	1
FR900359	affects phosphorylation	1
bisphenol F	affects cotreatment, increases expression	1
methylmercuric chloride	decreases expression	1
arsenite	affects binding, decreases reaction	1
sodium arsenite	decreases expression	1
butyraldehyde	decreases expression	1
beta-methylcholine	affects expression	1
cyanoginosin LR	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	increases reaction, affects binding	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	affects cotreatment, decreases expression	1
(+)-JQ1 compound	decreases expression	1

Clinical trials (associated diseases)

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