ING3

inhibitor of growth family member 3, the group of Tip60/Nua4 histone acetyltransferase complex subunits|PHD finger proteins

Basic information

Region (hg38): 7:120950763-120977216

Links

ENSG00000071243

∙ NCBI:54556 ∙ OMIM:607493 ∙ HGNC:14587 ∙ Uniprot:Q9NXR8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ING3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ING3 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					2 clinvar	2
missense			6 clinvar			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	2

Variants in ING3

This is a list of pathogenic ClinVar variants found in the ING3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Phenotype	Significance	ClinVar
7-120951195-C-T		Benign (Jun 21, 2018)	776256
7-120953357-A-C	not specified	Uncertain significance (Sep 10, 2024)	3529050
7-120966665-A-G	not specified	Uncertain significance (Jun 12, 2023)	2559678
7-120967539-T-C		Benign (Jun 16, 2018)	778332
7-120967999-C-A	not specified	Uncertain significance (Oct 04, 2022)	2316868
7-120968072-C-T	not specified	Uncertain significance (Nov 11, 2024)	3529051
7-120968087-C-T	not specified	Uncertain significance (Dec 12, 2023)	3109655
7-120969141-T-C	not specified	Uncertain significance (Oct 25, 2023)	3109656
7-120969162-C-A	not specified	Uncertain significance (Sep 20, 2024)	3529053
7-120970771-T-C	not specified	Uncertain significance (May 17, 2023)	2547183
7-120970792-A-G	not specified	Uncertain significance (Sep 26, 2024)	3529054
7-120970821-A-C	not specified	Uncertain significance (Jul 10, 2024)	3529052
7-120974806-A-G	not specified	Uncertain significance (Aug 07, 2023)	2612361

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ING3	protein_coding	protein_coding	ENST00000315870	12	26468

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000671	125733	0	2	125735	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.29	122	217	0.562	0.0000104	2726
Missense in Polyphen		49	115.96	0.42257		1483
Synonymous	-0.676	89	81.3	1.10	0.00000422	777
Loss of Function	4.73	2	29.9	0.0669	0.00000174	334

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: 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/H2AFZ from the nucleosome. {ECO:0000269|PubMed:12545155, ECO:0000269|PubMed:14966270, ECO:0000269|PubMed:24463511}.;
Disease: DISEASE: 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. {ECO:0000269|PubMed:12080476}. Note=The disease may be caused by mutations affecting the gene represented in this entry.;
Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

pRec: 0.107

Intolerance Scores

loftool: 0.103
rvis_EVS: -0.32
rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

pHI: 0.979
hipred: Y
hipred_score: 0.783
ghis: 0.644

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: H
gene_indispensability_pred: E
gene_indispensability_score: 0.994

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Ing3
Phenotype

Gene ontology

Biological process: regulation of growth;positive regulation of apoptotic process;histone H4 acetylation;histone H2A acetylation
Cellular component: Swr1 complex;nucleus;nucleoplasm;Piccolo NuA4 histone acetyltransferase complex;NuA4 histone acetyltransferase complex
Molecular function: histone acetyltransferase activity;methylated histone binding;metal ion binding