ING2

inhibitor of growth family member 2, the group of PHD finger proteins

Basic information

Region (hg38): 4:183505057-183512429

Previous symbols: [ "ING1L" ]

Links

ENSG00000168556 ∙ NCBI:3622 ∙ OMIM:604215 ∙ HGNC:6063 ∙ Uniprot:Q9H160 ∙ 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 ING2 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ING2 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in ING2

This is a list of pathogenic ClinVar variants found in the ING2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-183505211-C-A		not specified	Uncertain significance (Apr 27, 2023)
4-183505308-T-C		not specified	Uncertain significance (Feb 13, 2023)
4-183510545-G-A		not specified	Uncertain significance (Oct 20, 2023)
4-183510591-G-A		not specified	Uncertain significance (Sep 15, 2021)
4-183510761-A-G		not specified	Uncertain significance (Oct 26, 2022)
4-183510906-T-C		not specified	Uncertain significance (Dec 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ING2	protein_coding	protein_coding	ENST00000302327	2	6103

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.729	0.270	125601	0	1	125602	0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.74	87	146	0.595	0.00000767	1833
Missense in Polyphen		16	52.084	0.3072		616
Synonymous	0.470	48	52.3	0.917	0.00000263	485
Loss of Function	2.83	2	13.0	0.154	6.48e-7	166

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000621	0.0000621
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Seems to be involved in p53/TP53 activation and p53/TP53-dependent apoptotic pathways, probably by enhancing acetylation of p53/TP53. Component of a mSin3A-like corepressor complex, which is probably involved in deacetylation of nucleosomal histones. ING2 activity seems to be modulated by binding to phosphoinositides (PtdInsPs). {ECO:0000269|PubMed:11481424, ECO:0000269|PubMed:12859901}.
• Pathway: Senescence and Autophagy in Cancer;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;PI5P Regulates TP53 Acetylation;TGF_beta_Receptor;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53 (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.266
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.878
• hipred: Y
• hipred_score: 0.764
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.876

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ing2
• Phenotype: cellular phenotype; hematopoietic system phenotype; endocrine/exocrine gland phenotype; neoplasm; 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); reproductive system phenotype

Gene ontology

• Biological process: chromatin organization;regulation of transcription, DNA-templated;male meiosis I;signal transduction;spermatogenesis;spermatid development;negative regulation of cell population proliferation;flagellated sperm motility;positive regulation of transforming growth factor beta receptor signaling pathway;positive regulation of histone deacetylation;regulation of growth;positive regulation of transcription, DNA-templated;male germ-line stem cell asymmetric division;seminiferous tubule development;negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;regulation of cellular senescence;regulation of response to DNA damage stimulus
• Cellular component: nucleus;nucleoplasm;Golgi apparatus;cytosol;plasma membrane;Sin3 complex;CCAAT-binding factor complex
• Molecular function: DNA binding;chromatin binding;protein binding;methylated histone binding;phosphatidylinositol binding;protein-containing complex binding;metal ion binding