TP53I3

tumor protein p53 inducible protein 3

Basic information

Region (hg38): 2:24077433-24085861

Links

ENSG00000115129 ∙ NCBI:9540 ∙ OMIM:605171 ∙ HGNC:19373 ∙ Uniprot:Q53FA7 ∙ 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 TP53I3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TP53I3 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				5	3	8
missense			14	4	1	19
nonsense				2		2
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1	1		2
non coding				1		1
Total	0	0	14	12	4

Variants in TP53I3

This is a list of pathogenic ClinVar variants found in the TP53I3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-24077571-A-C		TP53I3-related disorder	Likely benign (Jan 22, 2024)
2-24077572-T-C		TP53I3-related disorder	Likely benign (Apr 09, 2024)
2-24077628-A-G		not specified	Uncertain significance (Mar 20, 2023)
2-24077647-G-C		not specified	Uncertain significance (Aug 05, 2024)
2-24077655-G-A		not specified	Uncertain significance (Sep 07, 2022)
2-24077693-T-C		TP53I3-related disorder	Benign (Oct 30, 2019)
2-24077699-G-A		TP53I3-related disorder • not specified	Likely benign (Feb 26, 2024)
2-24077769-A-G		TP53I3-related disorder	Likely benign (Sep 04, 2024)
2-24079447-A-C		TP53I3-related disorder	Likely benign (Oct 26, 2022)
2-24079456-A-G		TP53I3-related disorder	Likely benign (Mar 17, 2023)
2-24079475-A-G		not specified	Uncertain significance (Mar 29, 2023)
2-24079505-G-C		TP53I3-related disorder	Likely benign (Jul 19, 2022)
2-24079506-A-G		not specified	Uncertain significance (Nov 17, 2022)
2-24079514-G-T		not specified	Uncertain significance (May 07, 2024)
2-24079528-A-G		TP53I3-related disorder	Likely benign (Jan 18, 2024)
2-24079560-G-A		TP53I3-related disorder	Uncertain significance (Jul 18, 2024)
2-24079593-C-T		TP53I3-related disorder	Likely benign (Mar 05, 2022)
2-24079594-C-T		TP53I3-related disorder	Likely benign (May 30, 2024)
2-24080826-G-T		not specified	Uncertain significance (Nov 12, 2024)
2-24080835-C-T		TP53I3-related disorder	Benign (Dec 18, 2019)
2-24080836-G-A		TP53I3-related disorder • not specified	Uncertain significance (May 24, 2023)
2-24080853-C-G		TP53I3-related disorder	Likely benign (Aug 04, 2022)
2-24080899-A-T		not specified	Uncertain significance (Mar 18, 2024)
2-24080921-C-T		not specified	Uncertain significance (May 02, 2024)
2-24080953-C-A		not specified	Uncertain significance (Feb 21, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TP53I3	protein_coding	protein_coding	ENST00000238721	5	8429

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.95e-11	0.0343	125185	0	562	125747	0.00224

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.512	166	186	0.894	0.00000945	2126
Missense in Polyphen		47	56.436	0.8328		677
Synonymous	0.394	74	78.4	0.943	0.00000428	711
Loss of Function	-0.310	15	13.8	1.09	7.35e-7	151

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00775	0.00777
Ashkenazi Jewish	0.000992	0.000993
East Asian	0.000327	0.000326
Finnish	0.00106	0.00106
European (Non-Finnish)	0.00300	0.00298
Middle Eastern	0.000327	0.000326
South Asian	0.00102	0.00101
Other	0.00164	0.00147

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in the generation of reactive oxygen species (ROS). Has low NADPH-dependent beta-naphthoquinone reductase activity, with a preference for 1,2-beta-naphthoquinone over 1,4-beta-naphthoquinone. Has low NADPH-dependent diamine reductase activity (in vitro). {ECO:0000269|PubMed:19349281}.
• Pathway: p53 signaling pathway - Homo sapiens (human);TP53 Regulates Transcription of Cell Death Genes;Gene expression (Transcription);Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;p73 transcription factor network;TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain;Validated transcriptional targets of TAp63 isoforms;Transcriptional Regulation by TP53;Direct p53 effectors (Consensus)

Recessive Scores

• pRec: 0.139

Intolerance Scores

• loftool: 0.879
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.48

Haploinsufficiency Scores

• pHI: 0.218
• hipred: N
• hipred_score: 0.453
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Gene ontology

• Biological process: NADP metabolic process;regulation of apoptotic process;oxidation-reduction process
• Cellular component: cytosol
• Molecular function: NADPH:quinone reductase activity;protein homodimerization activity;quinone binding;NADPH binding