ING2

protein-coding

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

Gene summary

This gene is a member of the inhibitor of growth (ING) family. Members of the ING family associate with and modulate the activity of histone acetyltransferase (HAT) and histone deacetylase (HDAC) complexes and function in DNA repair and apoptosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2014]

Previous symbols:

ING1L

MANE transcript

NM_001564.4

Inheritance

—

ClinVar variants

U:18

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr4:183,505,058-183,512,429

External References & Databases

Ensembl (ENSG00000168556)

Transcript & Mutation Effects

hg38 • Region Span ~7.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ING2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 18

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001564.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			18 clinvar			18
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	18	0	0	18

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001564.4	RefSeq	NP_001555.1	2	MANE Select
ENST00000302327.4	Ensembl	ENSP00000307183.3	2	MANE Select
NM_001291959.2	RefSeq	NP_001278888.1	2	Standard
ENST00000412117.1	Ensembl	ENSP00000410291.1	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Senescence and Autophagy in Cancer
Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription
PI5P Regulates TP53 Acetylation

Biological Process

chromatin organization
regulation of transcription, DNA-templated
male meiosis I
signal transduction
spermatogenesis

Molecular Function

DNA binding
chromatin binding
protein binding
methylated histone binding
phosphatidylinositol binding

Cellular Component

nucleus
nucleoplasm
Golgi apparatus
cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000302327
Coding exons: 2
Length: 6103
Individuals with no LoFs: 125601
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125602
p: 0.00000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.74	87	146	0.595	0.00000767	1833
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000062	0.000062	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.130

Intolerance Scores

LoFtool: 0.266
RVIS EVS: -0.1
RVIS percentile EVS: 46.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.876

Gene Damage Prediction

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