TP53INP2

tumor protein p53 inducible nuclear protein 2

Basic information

Region (hg38): 20:34704339-34713439

Previous symbols: [ "C20orf110" ]

Links

ENSG00000078804 ∙ NCBI:58476 ∙ OMIM:617549 ∙ HGNC:16104 ∙ Uniprot:Q8IXH6 ∙ 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 TP53INP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TP53INP2 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in TP53INP2

This is a list of pathogenic ClinVar variants found in the TP53INP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-34708786-C-T		not specified	Uncertain significance (Nov 03, 2023)
20-34708788-G-C		not specified	Uncertain significance (Aug 28, 2021)
20-34708815-G-T		not specified	Uncertain significance (Sep 16, 2022)
20-34708845-C-G		not specified	Uncertain significance (Sep 26, 2023)
20-34709256-A-G		not specified	Uncertain significance (Dec 06, 2022)
20-34709257-G-A		not specified	Uncertain significance (Feb 03, 2022)
20-34709313-G-A		not specified	Uncertain significance (Dec 27, 2023)
20-34709316-G-C		not specified	Uncertain significance (Dec 21, 2021)
20-34709324-G-C		not specified	Uncertain significance (May 20, 2024)
20-34709371-G-C		not specified	Uncertain significance (Sep 17, 2021)
20-34709395-C-G		not specified	Uncertain significance (Jan 17, 2024)
20-34709427-A-T		not specified	Uncertain significance (Feb 17, 2024)
20-34709476-C-T		not specified	Uncertain significance (Mar 19, 2024)
20-34709508-G-A		not specified	Uncertain significance (Oct 26, 2022)
20-34710071-G-A		not specified	Uncertain significance (Mar 28, 2023)
20-34710075-G-A		not specified	Uncertain significance (Nov 08, 2022)
20-34710077-C-G		not specified	Uncertain significance (Apr 12, 2024)
20-34710080-G-A		not specified	Uncertain significance (Oct 24, 2023)
20-34710084-C-T		not specified	Uncertain significance (Jun 06, 2023)
20-34710110-C-G		not specified	Uncertain significance (Nov 17, 2022)
20-34710162-A-G		not specified	Uncertain significance (Dec 17, 2023)
20-34710165-G-A		not specified	Uncertain significance (Jun 17, 2024)
20-34710204-A-T		not specified	Uncertain significance (Aug 10, 2021)
20-34710207-C-A		not specified	Uncertain significance (Mar 04, 2024)
20-34710209-G-T		not specified	Uncertain significance (Jan 31, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TP53INP2	protein_coding	protein_coding	ENST00000374810	3	9150

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.812	0.184	113738	0	4	113742	0.0000176

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.318	107	117	0.917	0.00000531	1373
Missense in Polyphen		30	43.194	0.69454		517
Synonymous	0.470	49	53.4	0.918	0.00000257	486
Loss of Function	2.18	0	5.52	0.00	2.40e-7	64

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)	0.0000310	0.0000302
Middle Eastern	0.00	0.00
South Asian	0.0000337	0.0000335
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Dual regulator of transcription and autophagy. Positively regulates autophagy and is required for autophagosome formation and processing. May act as a scaffold protein that recruits MAP1LC3A, GABARAP and GABARAPL2 and brings them to the autophagosome membrane by interacting with VMP1 where, in cooperation with the BECN1-PI3-kinase class III complex, they trigger autophagosome development. Acts as a transcriptional activator of THRA. {ECO:0000269|PubMed:18030323, ECO:0000269|PubMed:19056683, ECO:0000269|PubMed:22470510}.
• Pathway: Autophagy - animal - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.102

Haploinsufficiency Scores

• pHI: 0.263
• hipred: N
• hipred_score: 0.235
• ghis: 0.477

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.160

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trp53inp2

Gene ontology

• Biological process: autophagosome assembly;osteoblast differentiation;tissue homeostasis;ubiquitin-dependent protein catabolic process;positive regulation of autophagy;positive regulation of transcription, DNA-templated;negative regulation of cellular protein localization
• Cellular component: nucleus;autophagosome;cytosol;PML body;cytoplasmic vesicle
• Molecular function: protein binding;ubiquitin binding