TP53TG5

TP53 target 5

Basic information

Region (hg38): 20:45372556-45407889

Previous symbols: [ "C20orf10" ]

Links

ENSG00000124251 ∙ NCBI:27296 ∙ OMIM:617316 ∙ HGNC:15856 ∙ Uniprot:Q9Y2B4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TP53TG5 gene.

• Inborn genetic diseases (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TP53TG5 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			14	4		18
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	4	0

Variants in TP53TG5

This is a list of pathogenic ClinVar variants found in the TP53TG5 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-45373915-A-G		not specified	Uncertain significance (Nov 15, 2021)
20-45375074-C-T		not specified	Uncertain significance (Dec 28, 2022)
20-45375095-G-A		not specified	Likely benign (Jan 03, 2022)
20-45375110-G-A		not specified	Uncertain significance (Aug 17, 2021)
20-45375136-C-T		not specified	Uncertain significance (Mar 01, 2023)
20-45375157-C-T		not specified	Uncertain significance (Jan 18, 2023)
20-45375232-T-C		not specified	Uncertain significance (Mar 16, 2022)
20-45375254-T-C		not specified	Likely benign (Jan 23, 2023)
20-45375254-T-G		not specified	Uncertain significance (Oct 26, 2022)
20-45375265-C-A		not specified	Uncertain significance (Jul 14, 2023)
20-45375319-G-A		not specified	Uncertain significance (Oct 14, 2023)
20-45375370-G-A		not specified	Uncertain significance (Jun 21, 2022)
20-45375381-T-A		not specified	Uncertain significance (Mar 13, 2023)
20-45375470-T-C		not specified	Uncertain significance (Mar 20, 2023)
20-45377293-C-T		not specified	Uncertain significance (Oct 26, 2022)
20-45377540-G-A		not specified	Likely benign (May 26, 2023)
20-45377549-C-T		not specified	Uncertain significance (May 04, 2022)
20-45377577-G-C		not specified	Uncertain significance (Aug 10, 2023)
20-45377589-C-T		not specified	Likely benign (May 09, 2023)
20-45406480-T-G		not specified	Uncertain significance (Oct 03, 2022)
20-45406527-G-A		not specified	Uncertain significance (Aug 17, 2022)
20-45406566-C-G		not specified	Uncertain significance (Sep 27, 2022)
20-45406590-C-T		not specified	Uncertain significance (Jan 06, 2023)
20-45406596-C-T		not specified	Uncertain significance (May 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TP53TG5	protein_coding	protein_coding	ENST00000372726	5	34004

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.44e-7	0.394	125603	1	144	125748	0.000577

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.487	152	170	0.895	0.0000104	1884
Missense in Polyphen		32	47.492	0.67379		511
Synonymous	-0.249	69	66.4	1.04	0.00000387	549
Loss of Function	0.616	11	13.4	0.819	7.63e-7	153

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000518	0.000514
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.00	0.00
Finnish	0.00392	0.00384
European (Non-Finnish)	0.000355	0.000352
Middle Eastern	0.00	0.00
South Asian	0.0000666	0.0000653
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a significant role in p53/TP53-mediating signaling pathway. {ECO:0000269|PubMed:10719363}.

Recessive Scores

• pRec: 0.0629

Intolerance Scores

• loftool: 0.841
• rvis_EVS: 0.69
• rvis_percentile_EVS: 85.18

Haploinsufficiency Scores

• pHI: 0.0658
• hipred: N
• hipred_score: 0.123
• ghis: 0.440

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000580

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trp53tg5

Gene ontology

• Biological process: negative regulation of cell growth;intracellular signal transduction
• Cellular component: nucleus;cytoplasm
• Molecular function: molecular_function