ING1

protein-coding

inhibitor of growth family member 1, the group of PHD finger proteins

Gene summary

This gene encodes a tumor suppressor protein that can induce cell growth arrest and apoptosis. The encoded protein is a nuclear protein that physically interacts with the tumor suppressor protein TP53 and is a component of the p53 signaling pathway. Reduced expression and rearrangement of this gene have been detected in various cancers. Multiple alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

MANE transcript

NM_198219.3

Inheritance

—

ClinVar variants

P:3U:33B:4

Top phenotype

Squamous cell carcinoma of the head and neck

gnomAD constraint

pLI —, LoF o/e 0.38

Max pathogenic AF

—

Genomic locus

chr13:110,712,736-110,723,339

External References & Databases

Ensembl (ENSG00000153487)

Transcript & Mutation Effects

hg38 • Region Span ~10.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

head and neck squamous cell carcinomaNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0010150

Submitter: Ambry Genetics

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to ING1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 86

Squamous cell carcinoma of the head and neckTotal: 3

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198219.3. 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					1 clinvar	1
missense	3 clinvar		33 clinvar	3 clinvar		39
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	3	0	33	3	1	40

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 17 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198219.3	RefSeq	NP_937862.1	2	MANE Select
ENST00000333219.9	Ensembl	ENSP00000328436.8	2	MANE Select
NM_001267728.1	RefSeq	NP_001254657.1	2	Standard
NM_005537.5	RefSeq	NP_005528.4	2	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Senescence and Autophagy in Cancer

Biological Process

cell cycle
negative regulation of cell population proliferation
regulation of cell death
negative regulation of cell growth
positive regulation of transcription, DNA-templated

Molecular Function

protein binding
methylated histone binding
metal ion binding

Cellular Component

nucleus

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000375774
Coding exons: 2
Length: 8339
Individuals with no LoFs: 122169
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 122170
p: 0.00000409

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.493	255	278	0.917	0.0000180	2690
Missense (PolyPhen)		35	112.65	0.31071		1031
Synonymous	-0.133	130	128	1.01	0.00000936	872
Loss of Function	2.26	6	15.7	0.383	8.04e-7	148

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
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)	0.0000091	0.0000091	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Cooperates with p53/TP53 in the negative regulatory pathway of cell growth by modulating p53-dependent transcriptional activation. Implicated as a tumor suppressor gene. {ECO:0000269|PubMed:9440695}.;
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:10866301}. Note=The disease is caused by mutations affecting the gene represented in this entry.;

Recessive Scores

pRec: 0.174

Intolerance Scores

LoFtool: 0.343
RVIS EVS: -0.51
RVIS percentile EVS: 21.56

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): H
Indispensability pred.: E
Indispensability score: 0.904

Gene Damage Prediction

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