TP53INP1

tumor protein p53 inducible nuclear protein 1

Basic information

Region (hg38): 8:94925971-94949378

Links

ENSG00000164938 ∙ NCBI:94241 ∙ OMIM:606185 ∙ HGNC:18022 ∙ Uniprot:Q96A56 ∙ 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 TP53INP1 gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TP53INP1 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			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in TP53INP1

This is a list of pathogenic ClinVar variants found in the TP53INP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-94930489-T-C		not specified	Uncertain significance (Oct 06, 2022)
8-94930495-C-T		not specified	Uncertain significance (Nov 12, 2021)
8-94930532-T-G		not specified	Uncertain significance (Dec 11, 2023)
8-94930570-C-T		not specified	Uncertain significance (Dec 08, 2023)
8-94930571-G-A		not specified	Uncertain significance (Mar 01, 2023)
8-94930573-C-G		not specified	Uncertain significance (Nov 21, 2023)
8-94930578-G-C		not specified	Uncertain significance (Dec 19, 2022)
8-94930594-G-A		not specified	Uncertain significance (Oct 25, 2023)
8-94930633-C-T		not specified	Uncertain significance (Dec 08, 2023)
8-94930699-T-C		not specified	Uncertain significance (Jul 08, 2022)
8-94939938-T-C		not specified	Uncertain significance (May 27, 2022)
8-94940019-G-A		not specified	Uncertain significance (Nov 15, 2021)
8-94940029-G-A		not specified	Uncertain significance (Jul 12, 2023)
8-94940029-G-C		not specified	Uncertain significance (Apr 12, 2023)
8-94940038-T-C		not specified	Uncertain significance (Sep 14, 2021)
8-94940109-C-A		not specified	Uncertain significance (Apr 07, 2023)
8-94940124-G-A		not specified	Uncertain significance (Oct 27, 2022)
8-94940158-G-A		not specified	Uncertain significance (Sep 14, 2022)
8-94940871-T-C		not specified	Likely benign (Jul 19, 2023)
8-94940888-G-C		not specified	Uncertain significance (Dec 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TP53INP1	protein_coding	protein_coding	ENST00000342697	3	23440

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000466	0.684	125712	0	36	125748	0.000143

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.337	123	134	0.918	0.00000689	1616
Missense in Polyphen		34	39.236	0.86656		470
Synonymous	0.268	40	42.2	0.947	0.00000191	428
Loss of Function	0.797	6	8.51	0.705	3.60e-7	109

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000786	0.000760
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000109	0.000109
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Antiproliferative and proapoptotic protein involved in cell stress response which acts as a dual regulator of transcription and autophagy. Acts as a positive regulator of autophagy. In response to cellular stress or activation of autophagy, relocates to autophagosomes where it interacts with autophagosome-associated proteins GABARAP, GABARAPL1/L2, MAP1LC3A/B/C and regulates autophagy. Acts as an antioxidant and plays a major role in p53/TP53-driven oxidative stress response. Possesses both a p53/TP53-independent intracellular reactive oxygen species (ROS) regulatory function and a p53/TP53-dependent transcription regulatory function. Positively regulates p53/TP53 and p73/TP73 and stimulates their capacity to induce apoptosis and regulate cell cycle. In response to double-strand DNA breaks, promotes p53/TP53 phosphorylation on 'Ser-46' and subsequent apoptosis. Acts as a tumor suppressor by inducing cell death by an autophagy and caspase-dependent mechanism. Can reduce cell migration by regulating the expression of SPARC. {ECO:0000269|PubMed:11511362, ECO:0000269|PubMed:22421968, ECO:0000269|PubMed:22470510}.
• Pathway: HTLV-I infection - Homo sapiens (human);miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;TP53 Regulates Transcription of Cell Death Genes;Gene expression (Transcription);Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;TP53 Regulates Transcription of Genes Involved in Cytochrome C Release;Regulation of TP53 Activity through Phosphorylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Direct p53 effectors (Consensus)

Recessive Scores

• pRec: 0.280

Intolerance Scores

• loftool: 0.841
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.404
• hipred: Y
• hipred_score: 0.728
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.825

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trp53inp1
• 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); liver/biliary system phenotype; immune system phenotype; digestive/alimentary phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: autophagosome assembly;apoptotic process;cell cycle arrest;negative regulation of cell population proliferation;response to heat;positive regulation of autophagy;negative regulation of gene expression;negative regulation of cell migration;cellular response to UV;regulation of apoptotic process;positive regulation of apoptotic process;positive regulation of transcription, DNA-templated;autophagic cell death;negative regulation of fibroblast proliferation;cellular response to ethanol;cellular response to hydroperoxide;cellular response to methyl methanesulfonate;cellular oxidant detoxification;regulation of signal transduction by p53 class mediator;negative regulation of myofibroblast differentiation
• Cellular component: nucleus;nucleoplasm;autophagosome;cytosol;PML body;cytoplasmic vesicle
• Molecular function: protein binding;antioxidant activity