TP53BP2

tumor protein p53 binding protein 2, the group of Protein phosphatase 1 regulatory subunits|Ankyrin repeat domain containing

Basic information

Region (hg38): 1:223779893-223845954

Links

ENSG00000143514 ∙ NCBI:7159 ∙ OMIM:602143 ∙ HGNC:12000 ∙ Uniprot:Q13625 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TP53BP2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TP53BP2 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	5
missense			74	5	2	81
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					2	2
Total	0	0	74	5	9

Variants in TP53BP2

This is a list of pathogenic ClinVar variants found in the TP53BP2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-223784159-G-A		not specified	Uncertain significance (Nov 25, 2024)
1-223784160-C-T		TP53BP2-related disorder	Benign (Mar 22, 2019)
1-223784174-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-223784207-T-C		not specified	Uncertain significance (Nov 08, 2024)
1-223784221-T-C		not specified	Uncertain significance (Dec 28, 2022)
1-223789137-G-C		not specified	Uncertain significance (Aug 02, 2021)
1-223789144-G-A		TP53BP2-related disorder	Benign (Feb 28, 2019)
1-223789168-T-C		TP53BP2-related disorder	Benign (Feb 16, 2018)
1-223792444-C-T		not specified	Uncertain significance (Oct 20, 2021)
1-223792454-G-C		not specified	Uncertain significance (Dec 27, 2023)
1-223792482-G-T		not specified	Uncertain significance (Sep 26, 2024)
1-223792505-G-C		TP53BP2-related disorder	Benign (Oct 18, 2019)
1-223795836-G-A		TP53BP2-related disorder	Benign (Jun 12, 2019)
1-223795838-T-C		not specified	Uncertain significance (May 17, 2023)
1-223795853-G-A		not specified	Uncertain significance (Apr 25, 2022)
1-223795871-C-T		not specified	Uncertain significance (Jun 22, 2024)
1-223795896-T-G		TP53BP2-related disorder	Likely benign (Apr 10, 2019)
1-223795902-T-G		TP53BP2-related disorder	Likely benign (Dec 02, 2019)
1-223795978-G-C		not specified	Uncertain significance (Mar 25, 2024)
1-223796026-T-C		not specified	Uncertain significance (Aug 20, 2024)
1-223796041-G-A		not specified	Uncertain significance (Jan 19, 2024)
1-223796084-C-T		not specified	Uncertain significance (Aug 27, 2024)
1-223796086-T-C		not specified	Uncertain significance (Oct 17, 2023)
1-223796132-C-T		not specified	Uncertain significance (Oct 25, 2023)
1-223796144-G-A		not specified	Uncertain significance (Aug 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TP53BP2	protein_coding	protein_coding	ENST00000343537	18	66074

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00255	0.997	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.89	498	632	0.788	0.0000356	7420
Missense in Polyphen		188	283.29	0.66364		3220
Synonymous	0.400	226	234	0.967	0.0000138	2186
Loss of Function	4.96	16	56.1	0.285	0.00000292	647

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000335	0.000332
Ashkenazi Jewish	0.000118	0.0000992
East Asian	0.000172	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000161	0.000158
Middle Eastern	0.000172	0.000109
South Asian	0.000197	0.000196
Other	0.000172	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator that plays a central role in regulation of apoptosis and cell growth via its interactions. Regulates TP53 by enhancing the DNA binding and transactivation function of TP53 on the promoters of proapoptotic genes in vivo. Inhibits the ability of APPBP1 to conjugate NEDD8 to CUL1, and thereby decreases APPBP1 ability to induce apoptosis. Impedes cell cycle progression at G2/M. Its apoptosis-stimulating activity is inhibited by its interaction with DDX42. {ECO:0000269|PubMed:11684014, ECO:0000269|PubMed:12694406, ECO:0000269|PubMed:19377511}.
• Pathway: Hippo signaling pathway - Homo sapiens (human);Gene expression (Transcription);Generic Transcription Pathway;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;Activation of PUMA and translocation to mitochondria;Activation of BH3-only proteins;Intrinsic Pathway for Apoptosis;Apoptosis;Programmed Cell Death;TP53 Regulates Transcription of Genes Involved in Cytochrome C Release;TP53 regulates transcription of several additional cell death genes whose specific roles in p53-dependent apoptosis remain uncertain;Regulation of TP53 Activity through Association with Co-factors;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Direct p53 effectors;TP53 Regulates Transcription of Death Receptors and Ligands (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.758
• rvis_EVS: -1.13
• rvis_percentile_EVS: 6.56

Haploinsufficiency Scores

• pHI: 0.461
• hipred: Y
• hipred_score: 0.706
• ghis: 0.564

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.816

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Trp53bp2
• Phenotype: craniofacial phenotype; cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype; 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); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); growth/size/body region phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; renal/urinary system phenotype; skeleton phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; neoplasm

Zebrafish Information Network

• Gene name: tp53bp2b
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: cell cycle;signal transduction;regulation of apoptotic process;negative regulation of cell cycle;intrinsic apoptotic signaling pathway by p53 class mediator;positive regulation of execution phase of apoptosis;positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway;positive regulation of neuron death;regulation of signal transduction by p53 class mediator
• Cellular component: nucleus;nucleoplasm;cytoplasm;mitochondrion;cytosol;cell junction;perinuclear region of cytoplasm
• Molecular function: p53 binding;SH3/SH2 adaptor activity;protein binding;SH3 domain binding;identical protein binding;NF-kappaB binding