ING4

inhibitor of growth family member 4, the group of PHD finger proteins

Basic information

Region (hg38): 12:6650300-6663142

Links

ENSG00000111653 ∙ NCBI:51147 ∙ OMIM:608524 ∙ HGNC:19423 ∙ Uniprot:Q9UNL4 ∙ 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 ING4 gene.

• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ING4 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						0
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	3	0	0

Variants in ING4

This is a list of pathogenic ClinVar variants found in the ING4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-6651380-G-A		not specified	Likely benign (Dec 22, 2023)
12-6652414-G-C		not specified	Uncertain significance (Feb 02, 2024)
12-6652666-G-A		not specified	Uncertain significance (Aug 02, 2021)
12-6652681-T-G		not specified	Uncertain significance (Dec 03, 2021)
12-6652731-C-T		not specified	Uncertain significance (Sep 07, 2022)
12-6653001-G-T		Malignant tumor of prostate	Uncertain significance (-)
12-6653305-C-G		not specified	Uncertain significance (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ING4	protein_coding	protein_coding	ENST00000396807	8	12869

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0290	0.962	125738	0	9	125747	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.81	88	151	0.584	0.00000871	1662
Missense in Polyphen		20	54.585	0.3664		621
Synonymous	0.873	42	49.8	0.843	0.00000259	436
Loss of Function	2.27	5	14.2	0.351	6.96e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000869	0.0000869
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.00000991	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.000108	0.0000980
Other	0.00	0.00

dbNSFP

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. Through chromatin acetylation it may function in DNA replication. May inhibit tumor progression by modulating the transcriptional output of signaling pathways which regulate cell proliferation. Can suppress brain tumor angiogenesis through transcriptional repression of RELA/NFKB3 target genes when complexed with RELA. May also specifically suppress loss of contact inhibition elicited by activated oncogenes such as MYC. Represses hypoxia inducible factor's (HIF) activity by interacting with HIF prolyl hydroxylase 2 (EGLN1). Can enhance apoptosis induced by serum starvation in mammary epithelial cell line HC11 (By similarity). {ECO:0000250|UniProtKB:Q8C0D7, ECO:0000269|PubMed:12750254, ECO:0000269|PubMed:15029197, ECO:0000269|PubMed:15251430, ECO:0000269|PubMed:15528276, ECO:0000269|PubMed:15897452, ECO:0000269|PubMed:16387653}.
• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.171

Intolerance Scores

• loftool: 0.115
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.4

Haploinsufficiency Scores

• pHI: 0.962
• hipred: Y
• hipred_score: 0.754
• ghis: 0.608

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.966

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ing4
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: DNA replication;protein acetylation;apoptotic process;DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator;cell cycle arrest;negative regulation of cell population proliferation;positive regulation of apoptotic process;histone H3 acetylation;histone H4-K5 acetylation;histone H4-K8 acetylation;histone H4-K12 acetylation;histone H4-K16 acetylation;negative regulation of transcription, DNA-templated;negative regulation of growth;positive regulation of nucleic acid-templated transcription
• Cellular component: histone acetyltransferase complex;nucleus;nucleoplasm;cytosol;intermediate filament cytoskeleton
• Molecular function: transcription coactivator activity;protein binding;methylated histone binding;metal ion binding