TP53I13

tumor protein p53 inducible protein 13

Basic information

Region (hg38): 17:29566052-29573157

Links

ENSG00000167543 ∙ NCBI:90313 ∙ ∙ HGNC:25102 ∙ Uniprot:Q8NBR0 ∙ 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 TP53I13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TP53I13 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			27	2		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	2	0

Variants in TP53I13

This is a list of pathogenic ClinVar variants found in the TP53I13 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-29566233-G-A		not specified	Uncertain significance (Apr 07, 2023)
17-29566248-G-A		not specified	Uncertain significance (Dec 15, 2023)
17-29566282-C-T		not specified	Uncertain significance (Apr 05, 2023)
17-29566329-G-T		not specified	Uncertain significance (Nov 14, 2023)
17-29566389-C-G		not specified	Uncertain significance (Jun 06, 2023)
17-29566402-C-A		not specified	Uncertain significance (Nov 22, 2021)
17-29566407-T-C		not specified	Uncertain significance (Oct 26, 2021)
17-29566417-G-A		not specified	Uncertain significance (Feb 12, 2024)
17-29566473-T-C		not specified	Uncertain significance (May 29, 2024)
17-29566528-C-T		not specified	Uncertain significance (Apr 26, 2023)
17-29566554-T-G		not specified	Uncertain significance (Dec 13, 2023)
17-29566677-G-C		not specified	Uncertain significance (May 26, 2024)
17-29566822-C-T		not specified	Uncertain significance (Dec 11, 2023)
17-29566857-G-T		not specified	Uncertain significance (Apr 24, 2024)
17-29566882-A-T		not specified	Uncertain significance (Apr 26, 2024)
17-29566921-C-G			Uncertain significance (Aug 01, 2022)
17-29566923-A-G		not specified	Uncertain significance (Mar 07, 2024)
17-29566957-A-G		not specified	Uncertain significance (May 09, 2024)
17-29568771-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-29568786-C-G		not specified	Uncertain significance (Mar 29, 2022)
17-29568807-G-T		not specified	Uncertain significance (Jun 21, 2021)
17-29568827-C-G		not specified	Uncertain significance (Dec 27, 2022)
17-29569048-G-A		not specified	Uncertain significance (Dec 08, 2021)
17-29569342-C-G		not specified	Uncertain significance (May 26, 2024)
17-29569345-G-A		not specified	Likely benign (Apr 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TP53I13	protein_coding	protein_coding	ENST00000301057	7	7106

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000112	0.955	124728	0	46	124774	0.000184

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0678	223	226	0.987	0.0000126	2421
Missense in Polyphen		72	77.245	0.9321		894
Synonymous	0.728	86	95.0	0.905	0.00000515	896
Loss of Function	1.81	9	17.0	0.528	9.32e-7	169

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000397	0.000395
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000326	0.000325
European (Non-Finnish)	0.000211	0.000203
Middle Eastern	0.00	0.00
South Asian	0.000198	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May act as a tumor suppressor. Inhibits tumor cell growth, when overexpressed. {ECO:0000269|PubMed:14767535}.

Recessive Scores

• pRec: 0.0901

Intolerance Scores

• loftool: 0.272
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.58

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.169
• ghis: 0.615

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.145

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trp53i13

Gene ontology

• Biological process: response to UV;response to organic cyclic compound;response to drug;negative regulation of cell cycle
• Cellular component: cytoplasm;plasma membrane;integral component of membrane
• Molecular function: molecular_function