ING1

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

Basic information

Region (hg38): 13:110712735-110723339

Links

ENSG00000153487 ∙ NCBI:3621 ∙ OMIM:601566 ∙ HGNC:6062 ∙ Uniprot:Q9UK53 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• head and neck squamous cell carcinoma (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ING1 gene.

• Inborn genetic diseases (26 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ING1 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					1	1
missense			24	2		26
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	2	2

Variants in ING1

This is a list of pathogenic ClinVar variants found in the ING1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-110715453-G-T		not specified	Uncertain significance (May 27, 2022)
13-110715552-C-A		not specified	Uncertain significance (Aug 15, 2023)
13-110715589-G-A		not specified	Uncertain significance (Nov 21, 2022)
13-110715634-C-G		not specified	Uncertain significance (Jun 06, 2023)
13-110715673-C-T		not specified	Uncertain significance (Mar 23, 2022)
13-110715709-C-T		not specified	Uncertain significance (Sep 06, 2022)
13-110715720-A-C		not specified	Uncertain significance (Oct 27, 2022)
13-110715724-C-G		not specified	Uncertain significance (Jan 30, 2024)
13-110715768-T-TC			Benign (Jul 17, 2018)
13-110715786-C-T		not specified	Uncertain significance (Jul 30, 2023)
13-110715801-T-C		not specified	Likely benign (Apr 05, 2023)
13-110715801-T-G		not specified	Uncertain significance (Nov 02, 2021)
13-110715807-G-A		not specified	Uncertain significance (Feb 14, 2023)
13-110715819-C-T		not specified	Uncertain significance (Jan 08, 2024)
13-110715837-C-T		not specified	Uncertain significance (Feb 16, 2023)
13-110715852-C-T		not specified	Uncertain significance (Jan 17, 2024)
13-110715855-G-A		not specified	Uncertain significance (Dec 06, 2023)
13-110715870-G-T		not specified	Uncertain significance (Nov 27, 2023)
13-110715882-G-C		not specified	Uncertain significance (Sep 16, 2021)
13-110715891-G-C		not specified	Uncertain significance (May 05, 2023)
13-110715912-T-C		not specified	Uncertain significance (Feb 01, 2023)
13-110715953-G-T		not specified	Uncertain significance (Jun 14, 2023)
13-110715990-C-T		not specified	Uncertain significance (Aug 12, 2021)
13-110715999-C-T		not specified	Uncertain significance (Feb 28, 2024)
13-110719416-C-G		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ING1	protein_coding	protein_coding	ENST00000375774	2	8339

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00967	0.981	122169	0	1	122170	0.00000409

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.493	255	278	0.917	0.0000180	2690
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000914	0.00000914
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

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.
• Pathway: Senescence and Autophagy in Cancer (Consensus)

Recessive Scores

• pRec: 0.174

Intolerance Scores

• loftool: 0.343
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.56

Haploinsufficiency Scores

• pHI: 0.789
• hipred: Y
• hipred_score: 0.701
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.904

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ing1
• Phenotype: neoplasm; 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); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); immune system phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• 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
• Cellular component: nucleus
• Molecular function: protein binding;methylated histone binding;metal ion binding