ING3

Summary

ING3 (inhibitor of growth family member 3, HGNC:14587) is a protein-coding gene on chromosome 7q31.31, encoding Inhibitor of growth protein 3 (Q9NXR8). Component of the NuA4 histone acetyltransferase (HAT) complex which is involved in transcriptional activation of select genes principally by acetylation of nucleosomal histones H4 and H2A. It is a selective cancer dependency (DepMap: 48.1% of cell lines).

The protein encoded by this gene is similar to ING1, a tumor suppressor protein that can interact with TP53, inhibit cell growth, and induce apoptosis. This protein contains a PHD-finger, which is a common motif in proteins involved in chromatin remodeling. This gene can activate p53 trans-activated promoters, including promoters of p21/waf1 and bax. Overexpression of this gene has been shown to inhibit cell growth and induce apoptosis. Allelic loss and reduced expression of this gene were detected in head and neck cancers. Two alternatively spliced transcript variants encoding different isoforms have been observed.

Source: NCBI Gene 54556 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 32 total
• Cancer dependency (DepMap): dependent in 48.1% of screened cell lines
• MANE Select transcript: NM_019071

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:14587
Approved symbol	ING3
Name	inhibitor of growth family member 3
Location	7q31.31
Locus type	gene with protein product
Status	Approved
Aliases	p47ING3, FLJ20089, Eaf4, MEAF4
Ensembl gene	ENSG00000071243
Ensembl biotype	protein_coding
OMIM	607493
Entrez	54556

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 1 nonsense_mediated_decay, 1 retained_intron

ENST00000315870, ENST00000339121, ENST00000427726, ENST00000431467, ENST00000445699, ENST00000497502, ENST00000875858, ENST00000875859

RefSeq mRNA: 2 — MANE Select: NM_019071 NM_019071, NM_198267

CCDS: CCDS35497, CCDS5778

Canonical transcript exons

ENST00000315870 — 12 exons

Exon	Start	End
ENSE00000881961	120951164	120951235
ENSE00000881962	120953304	120953404
ENSE00000881963	120955559	120955624
ENSE00001344212	120974728	120977216
ENSE00001344252	120964742	120964838
ENSE00001928540	120950777	120950924
ENSE00003519604	120973205	120973243
ENSE00003532124	120967529	120967648
ENSE00003536918	120969011	120969204
ENSE00003616283	120966626	120966697
ENSE00003630222	120967934	120968091
ENSE00003645307	120970688	120970880

Expression profiles

Bgee: expression breadth ubiquitous, 289 present calls, max score 99.28.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 15.7185 / max 868.3864, expressed in 1767 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
80778	13.4075	1752
80780	1.4558	681
80779	0.7431	416
80781	0.1121	48

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
secondary oocyte	CL:0000655	99.28	gold quality
oocyte	CL:0000023	97.86	gold quality
trabecular bone tissue	UBERON:0002483	92.30	gold quality
monocyte	CL:0000576	91.63	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	91.57	gold quality
mononuclear cell	CL:0000842	91.25	gold quality
leukocyte	CL:0000738	90.98	gold quality
calcaneal tendon	UBERON:0003701	90.20	gold quality
bone marrow	UBERON:0002371	89.98	gold quality
bone element	UBERON:0001474	89.90	gold quality
cauda epididymis	UBERON:0004360	89.75	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.58	gold quality
germinal epithelium of ovary	UBERON:0001304	89.35	gold quality
adrenal tissue	UBERON:0018303	89.33	gold quality
parietal pleura	UBERON:0002400	89.19	gold quality
ventricular zone	UBERON:0003053	89.15	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	88.97	gold quality
visceral pleura	UBERON:0002401	88.65	gold quality
cranial nerve II	UBERON:0000941	88.60	gold quality
lower lobe of lung	UBERON:0008949	88.59	gold quality
caput epididymis	UBERON:0004358	88.52	gold quality
pleura	UBERON:0000977	88.16	gold quality
corpus epididymis	UBERON:0004359	87.95	gold quality
palpebral conjunctiva	UBERON:0001812	87.21	gold quality
epithelium of nasopharynx	UBERON:0001951	86.34	gold quality
nasopharynx	UBERON:0001728	86.32	gold quality
rectum	UBERON:0001052	85.92	gold quality
ganglionic eminence	UBERON:0004023	85.82	gold quality
granulocyte	CL:0000094	85.79	gold quality
amniotic fluid	UBERON:0000173	85.74	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.15
E-MTAB-7303	no	222.33

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): TXK

miRNA regulators (miRDB)

132 targeting ING3, 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-3163	100.00	77.23	8605
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-4668-3P	100.00	68.74	2635
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-4282	99.99	75.36	6408
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-548AN	99.97	70.91	2817
HSA-MIR-302C-5P	99.97	72.56	3642
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548AA	99.96	70.64	3753
HSA-MIR-548AP-3P	99.96	70.64	3753
HSA-MIR-548T-3P	99.96	70.64	3753
HSA-MIR-3910	99.95	71.13	2227
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-101-3P	99.94	75.03	2230
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-1297	99.91	73.41	3162
HSA-MIR-219A-5P	99.91	73.36	735
HSA-MIR-6809-3P	99.91	71.45	3814

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 48.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 19)

• Allelic loss and reduced expression of the ING3, a candidate tumor suppressor gene at 7q31, in human head and neck cancers. (PMID:12080476)
• we have isolated a novel ING family gene, p47ING3, which modulates p53-mediated transcription, cell cycle control, and apoptosis. The p47ING3 gene is located at chromosome 7q31.3 and consists of 12 exons that encode 418 amino acids (PMID:12545155)
• ING3 may be an important marker for human melanoma progression and prognosis as well as a potential therapeutic target. (PMID:17634537)
• ING3 would function as a potential tumor suppressor molecule and that low levels of ING3 may indicate an aggressive nature of head and neck cancer. (PMID:18081876)
• Data show that ING3 is degraded by the ubiquitin-proteasome pathway through the SCF(Skp2) complex. (PMID:19935701)
• that ING3 may be an important marker for human hepatocellular carcinoma progression and prognosis, as well as a potential therapeutic target. (PMID:22550337)
• Downregulated ING3 expression might play an important role in colorectal adenoma-adenocarcinoma sequence. (PMID:24927342)
• ING3 levels may serve as a surrogate for growth rate, and suggest possible roles for ING3 in growth and self renewal and related diseases such as cancer. (PMID:25819753)
• High ING3 expression is associated with prostate cancer. (PMID:26803516)
• results reveal the molecular mechanism of H3K4me3 selection by the ING3PHD and suggest that this interaction is important for mediating ING3 tumor suppressive activities. (PMID:27281824)
• Data show that ING3 associates with gene promoters to regulate a transcriptional network that is required for cellular proliferation. Importantly, ING3 elevated copy number and protein levels in cancer patients, particularly in treatment-resistant patients, designate ING3 as a novel marker of poor survival for cancer patients and an unsuspected oncoprotein. (PMID:29381681)
• ING3 is required for ATM signaling and DNA repair in response to DNA double strand breaks. (PMID:30804473)
• Downregulation of nuclear ING3 expression and translocalization to cytoplasm promotes tumorigenesis and progression in head and neck squamous cell carcinoma (HNSCC). (PMID:31886514)
• Nuclear localization of ING3 is required to suppress melanoma cell migration, invasion and angiogenesis. (PMID:32334834)
• A Novel Splice Variant of the Inhibitor of Growth 3 Lacks the Plant Homeodomain and Regulates Epithelial-Mesenchymal Transition in Prostate Cancer Cells. (PMID:34439818)
• ING Tumour Suppressors and ING Splice Variants as Coregulators of the Androgen Receptor Signalling in Prostate Cancer. (PMID:34685579)
• ING3 and ING4 immunoexpression and their relation to the development of benign odontogenic lesions. (PMID:34787253)
• Inhibitor of growth protein 3 epigenetically silences endogenous retroviral elements and prevents innate immune activation. (PMID:34791430)
• ING3 inhibits the malignant progression of lung adenocarcinoma by negatively regulating ITGB4 expression to inactivate Src/FAK signaling. (PMID:38281617)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ing3	ENSDARG00000034326
mus_musculus	Ing3	ENSMUSG00000029670
rattus_norvegicus	Ing3	ENSRNOG00000005496
drosophila_melanogaster	Ing3	FBGN0030945

Paralogs (4): ING4 (ENSG00000111653), ING1 (ENSG00000153487), ING5 (ENSG00000168395), ING2 (ENSG00000168556)

Protein

Protein identifiers

Inhibitor of growth protein 3 — Q9NXR8 (reviewed: Q9NXR8)

Alternative names: p47ING3

All UniProt accessions (3): Q9NXR8, A0A0C4DG38, E7ET07

UniProt curated annotations — full annotation on UniProt →

Function. Component of the NuA4 histone acetyltransferase (HAT) complex which is involved in transcriptional activation of select genes principally by acetylation of nucleosomal histones H4 and H2A. This modification may both alter nucleosome - DNA interactions and promote interaction of the modified histones with other proteins which positively regulate transcription. This complex may be required for the activation of transcriptional programs associated with oncogene and proto-oncogene mediated growth induction, tumor suppressor mediated growth arrest and replicative senescence, apoptosis, and DNA repair. NuA4 may also play a direct role in DNA repair when directly recruited to sites of DNA damage. Component of a SWR1-like complex that specifically mediates the removal of histone H2A.Z/H2AZ1 from the nucleosome.

Subunit / interactions. Interacts with H3K4me3 and to a lesser extent with H3K4me2. Component of the NuA4 histone acetyltransferase complex which contains the catalytic subunit KAT5/TIP60 and the subunits EP400, TRRAP/PAF400, BRD8/SMAP, EPC1, DMAP1/DNMAP1, RUVBL1/TIP49, RUVBL2, ING3, actin, ACTL6A/BAF53A, MORF4L1/MRG15, MORF4L2/MRGX, MRGBP, YEATS4/GAS41, VPS72/YL1 and MEAF6. The NuA4 complex interacts with MYC and the adenovirus E1A protein. HTATTIP/TIP60, EPC1, and ING3 together constitute a minimal HAT complex termed Piccolo NuA4. Component of a SWR1-like complex.

Subcellular location. Nucleus.

Tissue specificity. Expressed in brain, heart, kidney, liver, lung, ovaries, placenta, prostate, skeletal muscle, small intestine, spleen, testis and thymus.

Disease relevance. Squamous cell carcinoma of the head and neck (HNSCC) [MIM:275355] A non-melanoma skin cancer affecting the head and neck. The hallmark of cutaneous SCC is malignant transformation of normal epidermal keratinocytes. The disease may be caused by variants affecting the gene represented in this entry.

Domain organisation. The PHD-type zinc finger mediates the binding to H3K4me3.

Miscellaneous. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay.

Similarity. Belongs to the ING family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q9NXR8-1	1	yes
Q9NXR8-2	2
Q9NXR8-3	3

RefSeq proteins (2): NP_061944, NP_938008 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001965	Znf_PHD	Domain
IPR011011	Znf_FYVE_PHD	Homologous_superfamily
IPR013083	Znf_RING/FYVE/PHD	Homologous_superfamily
IPR019786	Zinc_finger_PHD-type_CS	Conserved_site
IPR019787	Znf_PHD-finger	Domain
IPR024610	ING_N_histone-binding	Domain
IPR028651	ING_fam	Family
IPR042020	ING3_PHD	Domain

Pfam: PF12998

UniProt features (37 total): binding site 8, site 4, cross-link 4, splice variant 4, sequence conflict 3, modified residue 2, region of interest 2, strand 2, helix 2, compositionally biased region 2, chain 1, zinc finger region 1, sequence variant 1, turn 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
7ZMX	X-RAY DIFFRACTION	1.2
8COK	X-RAY DIFFRACTION	2.91
1X4I	SOLUTION NMR

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9NXR8-F1	65.68	0.24

Functional residue map

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

Catalytic / active sites (4): 362 (histone h3k4me3 binding); 373 (histone h3k4me3 binding); 377 (histone h3k4me3 binding); 385 (histone h3k4me3 binding)

Ligand- & substrate-binding residues (8): 387; 390; 403; 406; 363; 365; 376; 381

Post-translational modifications (6): 181, 264, 148, 165, 167, 256

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: 312 (showing top): GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR, E2F_Q4, RRAGTTGT_UNKNOWN, GOBP_REGULATION_OF_DNA_RECOMBINATION, HORIUCHI_WTAP_TARGETS_DN, TAATAAT_MIR126, E2F4DP1_01, GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GTTAAAG_MIR302B, CREBP1_Q2, GOBP_REGULATION_OF_DOUBLE_STRAND_BREAK_REPAIR_VIA_HOMOLOGOUS_RECOMBINATION, GOBP_REGULATION_OF_DNA_REPAIR, CTCTAGA_MIR526C_MIR518F_MIR526A, CREB_Q4, GGGCATT_MIR365

GO Biological Process (8): regulation of apoptotic process (GO:0042981), positive regulation of DNA-templated transcription (GO:0045893), positive regulation of transcription by RNA polymerase II (GO:0045944), regulation of cell cycle (GO:0051726), positive regulation of double-strand break repair via homologous recombination (GO:1905168), regulation of double-strand break repair (GO:2000779), chromatin organization (GO:0006325), chromatin remodeling (GO:0006338)

GO Molecular Function (10): zinc ion binding (GO:0008270), histone H4K5 acetyltransferase activity (GO:0043995), histone H4K8 acetyltransferase activity (GO:0043996), histone H4K12 acetyltransferase activity (GO:0043997), histone H4K16 acetyltransferase activity (GO:0046972), histone H3K4me3 reader activity (GO:0140002), protein binding (GO:0005515), histone H4 acetyltransferase activity (GO:0010485), histone H2A acetyltransferase activity (GO:0043998), metal ion binding (GO:0046872)

GO Cellular Component (6): nucleosome (GO:0000786), Swr1 complex (GO:0000812), nucleus (GO:0005634), nucleoplasm (GO:0005654), piccolo histone acetyltransferase complex (GO:0032777), NuA4 histone acetyltransferase complex (GO:0035267)

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
histone H4 acetyltransferase activity	4
histone acetyltransferase activity	2
apoptotic process	1
regulation of programmed cell death	1
DNA-templated transcription	1
regulation of DNA-templated transcription	1
positive regulation of RNA biosynthetic process	1
regulation of transcription by RNA polymerase II	1
transcription by RNA polymerase II	1
positive regulation of DNA-templated transcription	1
cell cycle	1
regulation of cellular process	1
double-strand break repair via homologous recombination	1
regulation of double-strand break repair via homologous recombination	1
positive regulation of DNA recombination	1
positive regulation of double-strand break repair	1
regulation of DNA repair	1
double-strand break repair	1
cellular component organization	1
chromatin organization	1
transition metal ion binding	1
histone H3 reader activity	1
binding	1
cation binding	1
chromatin	1
protein-DNA complex	1
histone deacetylase complex	1
nuclear chromosome	1
INO80-type complex	1
intracellular membrane-bounded organelle	1
nuclear lumen	1
cellular anatomical structure	1
protein-containing complex	1
H4/H2A histone acetyltransferase complex	1

Protein interactions and networks

STRING

1660 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ING3	MORF4L1	Q9UBU8	933
ING3	H3-3A	P06351	931
ING3	H3C1	P02295	927
ING3	H3-4	Q16695	927
ING3	H3-7	Q5TEC6	927
ING3	H3-5	Q6NXT2	927
ING3	H3C14	Q71DI3	927
ING3	KAT5	Q92993	926
ING3	BRD8	Q9H0E9	912
ING3	SIN3A	Q96ST3	886
ING3	MEAF6	Q9HAF1	872
ING3	SAP30	O75446	847
ING3	YEATS4	O95619	845
ING3	HDAC1	Q13547	803
ING3	TRRAP	Q9Y4A5	803

IntAct

103 interactions, top by confidence:

A	B	Type	Score
RUVBL1	ZNHIT1	psi-mi:“MI:0914”(association)	0.860
MRGBP	YEATS4	psi-mi:“MI:0914”(association)	0.840
RUVBL2	ZNHIT1	psi-mi:“MI:0914”(association)	0.810
YEATS4	ZNHIT1	psi-mi:“MI:0914”(association)	0.790
H2AZ1	ZNHIT1	psi-mi:“MI:0914”(association)	0.770
TRRAP	ATXN7	psi-mi:“MI:0914”(association)	0.740
MBTD1	YEATS4	psi-mi:“MI:0914”(association)	0.730
MBTD1	MORF4L2	psi-mi:“MI:0914”(association)	0.730
MORF4L1	SIN3B	psi-mi:“MI:0914”(association)	0.730
ACTL6A	ZNHIT1	psi-mi:“MI:0914”(association)	0.720
VPS72	ZNHIT1	psi-mi:“MI:0914”(association)	0.690
H2BC1	PPM1G	psi-mi:“MI:0914”(association)	0.640
RUVBL2	POLR3A	psi-mi:“MI:0914”(association)	0.640
RUVBL1	POLR3A	psi-mi:“MI:0914”(association)	0.640
MORF4L2	YEATS4	psi-mi:“MI:0914”(association)	0.640
FOXR1	YEATS4	psi-mi:“MI:0914”(association)	0.640
KPNA1	TCERG1	psi-mi:“MI:0914”(association)	0.640
EPC2	YEATS4	psi-mi:“MI:0914”(association)	0.640

BioGRID (189): TEX11 (Two-hybrid), TRIM54 (Two-hybrid), USHBP1 (Two-hybrid), ING3 (Affinity Capture-MS), ING3 (Affinity Capture-MS), ING3 (Affinity Capture-MS), ING3 (Affinity Capture-MS), ING3 (Affinity Capture-MS), ING3 (Affinity Capture-MS), ING3 (Affinity Capture-MS), ING3 (Affinity Capture-MS), HSPA5 (Affinity Capture-MS), PLD1 (Affinity Capture-MS), SNRPA1 (Affinity Capture-MS), VPS72 (Affinity Capture-MS)

ESM2 similar proteins: A1L209, A2AWT3, B0W8L4, B1PM81, B3M881, B3NHQ1, B4GZZ4, B4IFU5, B4J1U4, B4J1U5, B4KY72, B4LDA6, B4MVH6, B4PJ01, B4QPV0, F4IDY7, O94818, O94880, P61406, P97496, Q08AX9, Q14CW9, Q17CJ5, Q2LYX9, Q3UG20, Q498T3, Q5RBA1, Q5RIX9, Q5TYQ8, Q5ZK36, Q5ZKG2, Q66KD5, Q69ZW3, Q6DD45, Q6DFC8, Q6P2L6, Q7PXG4, Q7ZUF2, Q7ZX31, Q8IZD2

Diamond homologs: B3H615, O42871, O74736, P38806, P50947, Q08465, Q3T095, Q498T3, Q54PN9, Q5AHB8, Q5RBA1, Q5ZK36, Q5ZKY4, Q66KD5, Q6CXN0, Q757W2, Q7ZX31, Q8C0D7, Q8VEK6, Q8WYH8, Q9D8Y8, Q9LIQ6, Q9NXR8, Q9QXV3, Q9UK53, Q9UNL4, Q6BNL6, Q6C5V7, Q9ESK4, Q9H160, Q9VJY8, A3QMD7, Q6FSB1, A0A286Y9D1, B2KF05, B2RRD7, G5E8P1, O54826, O74759, O75164

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
ING3	“form complex”	“NuA4 complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 88 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	20	24.4×	2e-20
Chromatin organization	15	18.8×	2e-13
Chromatin modifying enzymes	15	16.7×	1e-12
Formation of the beta-catenin:TCF transactivating complex	7	12.9×	1e-04

GO biological processes:

GO term	Partners	Fold	FDR
regulation of double-strand break repair	15	103.8×	3e-25
positive regulation of double-strand break repair via homologous recombination	15	68.4×	4e-22
regulation of DNA replication	8	34.9×	4e-09
regulation of DNA repair	7	23.0×	1e-06
positive regulation of DNA repair	5	21.3×	1e-04
regulation of apoptotic process	17	16.9×	1e-14
regulation of cell cycle	19	16.9×	3e-16
chromatin remodeling	13	11.3×	6e-09

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	23
Likely benign	0
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

1361 predictions. Top by Δscore:

Variant	Effect	Δscore
7:120950920:GGAAA:G	donor_gain	1.0000
7:120950921:GAAA:G	donor_gain	1.0000
7:120950921:GAAAG:G	donor_gain	1.0000
7:120950922:A:T	donor_gain	1.0000
7:120950925:G:GG	donor_gain	1.0000
7:120951162:A:AG	acceptor_gain	1.0000
7:120951162:AGT:A	acceptor_gain	1.0000
7:120951163:G:GG	acceptor_gain	1.0000
7:120951163:GT:G	acceptor_gain	1.0000
7:120951163:GTG:G	acceptor_gain	1.0000
7:120951231:GCAGA:G	donor_gain	1.0000
7:120951234:GA:G	donor_gain	1.0000
7:120951236:G:GG	donor_gain	1.0000
7:120953296:T:G	acceptor_gain	1.0000
7:120953299:CATAG:C	acceptor_loss	1.0000
7:120953302:A:AG	acceptor_gain	1.0000
7:120953302:AGA:A	acceptor_loss	1.0000
7:120953303:G:GA	acceptor_gain	1.0000
7:120953303:GAT:G	acceptor_gain	1.0000
7:120953401:AAAA:A	donor_gain	1.0000
7:120953402:AAAGT:A	donor_loss	1.0000
7:120953403:AA:A	donor_gain	1.0000
7:120953403:AAGTA:A	donor_loss	1.0000
7:120953404:AGTA:A	donor_loss	1.0000
7:120953405:G:GG	donor_gain	1.0000
7:120953406:T:G	donor_loss	1.0000
7:120955555:TCAG:T	acceptor_loss	1.0000
7:120955556:CAGG:C	acceptor_loss	1.0000
7:120955557:A:AG	acceptor_gain	1.0000
7:120955557:A:G	acceptor_loss	1.0000

AlphaMissense

2731 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:120950907:T:A	L4Q	1.000
7:120950907:T:C	L4P	1.000
7:120950909:G:A	E5K	1.000
7:120950910:A:T	E5V	1.000
7:120950912:G:C	D6H	1.000
7:120950913:A:C	D6A	1.000
7:120950913:A:G	D6G	1.000
7:120950913:A:T	D6V	1.000
7:120950919:T:C	L8P	1.000
7:120950921:G:A	E9K	1.000
7:120951176:T:C	L14P	1.000
7:120951179:C:A	P15H	1.000
7:120951179:C:G	P15R	1.000
7:120951179:C:T	P15L	1.000
7:120951188:T:C	L18P	1.000
7:120951191:G:C	R19P	1.000
7:120951197:G:C	R21P	1.000
7:120951209:T:A	M25K	1.000
7:120951209:T:G	M25R	1.000
7:120951211:C:A	R26S	1.000
7:120951212:G:C	R26P	1.000
7:120951220:G:C	D29H	1.000
7:120951221:A:T	D29V	1.000
7:120951224:T:C	L30P	1.000
7:120953319:T:C	L39P	1.000
7:120955583:G:C	A76P	1.000
7:120955592:A:G	K79E	1.000
7:120955594:G:C	K79N	1.000
7:120955594:G:T	K79N	1.000
7:120955596:T:A	V80D	1.000

dbSNP variants (sampled 300 via entrez): RS1000154375 (7:120949897 C>T), RS1000206236 (7:120950065 GATTATT>G,GATT,GATTATTATT), RS1000244987 (7:120976465 A>G), RS1000303065 (7:120956622 T>G), RS1000310117 (7:120950675 G>A,T), RS1000313755 (7:120962680 C>T), RS1000324104 (7:120958823 ACT>A), RS1000438594 (7:120957008 A>G), RS1000577227 (7:120950560 G>C), RS1000638798 (7:120958124 C>T), RS1000741172 (7:120971350 G>A), RS1000771327 (7:120958339 C>T), RS1001059989 (7:120954205 C>T), RS1001122486 (7:120964534 T>G), RS1001172192 (7:120949041 C>T)

Disease associations

OMIM: gene MIM:607493 | 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

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects expression, decreases expression, increases expression	4
Arsenic	decreases expression, increases abundance, affects expression, affects cotreatment	2
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, decreases expression	2
Particulate Matter	affects cotreatment, 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
TAK-243	increases sumoylation	1
dicrotophos	decreases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
propionaldehyde	decreases expression	1
bisphenol A	decreases expression	1
trichostatin A	decreases expression	1
beta-lapachone	increases expression, decreases expression	1
tris(1,3-dichloro-2-propyl)phosphate	increases expression	1
sodium arsenite	affects cotreatment, decreases expression, increases abundance	1
butyraldehyde	decreases expression	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
ferrous chloride	decreases expression	1
resorcinol	decreases expression	1
beta-methylcholine	affects expression	1
pentanal	decreases expression	1
di-n-butylphosphoric acid	affects expression	1
glycidamide	decreases expression	1
CGP 52608	affects binding, increases reaction	1
entinostat	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
torcetrapib	increases expression	1
abrine	increases expression	1

Clinical trials (associated diseases)

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