ING4
inhibitor of growth family member 4, the group of PHD finger proteins
Basic information
Region (hg38): 12:6650301-6663142
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (16 variants)
- Prostate_cancer (1 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. These statistics are base on transcript: NM_000016162.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 16 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 16 | 1 | 0 |
Loading clinvar variants...
GnomAD
Source:
| 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:
- 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