TNKS1BP1

tankyrase 1 binding protein 1, the group of CCR4-NOT transcription complex

Basic information

Region (hg38): 11:57299638-57324952

Links

ENSG00000149115 ∙ NCBI:85456 ∙ OMIM:607104 ∙ HGNC:19081 ∙ Uniprot:Q9C0C2 ∙ 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 TNKS1BP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNKS1BP1 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				3	2	5
missense			114	6		120
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	114	9	2

Variants in TNKS1BP1

This is a list of pathogenic ClinVar variants found in the TNKS1BP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-57300932-C-A		not specified	Uncertain significance (Feb 23, 2023)
11-57300968-G-T		not specified	Uncertain significance (Feb 15, 2023)
11-57301026-G-A		not specified	Uncertain significance (Aug 13, 2021)
11-57301029-G-A		not specified	Likely benign (Apr 17, 2024)
11-57301884-G-A		not specified	Uncertain significance (Dec 20, 2022)
11-57301892-G-C		not specified	Uncertain significance (Feb 28, 2023)
11-57301938-G-A		not specified	Uncertain significance (Nov 13, 2023)
11-57302118-G-A		not specified	Uncertain significance (Oct 26, 2022)
11-57302146-T-A		not specified	Uncertain significance (Sep 27, 2022)
11-57302155-C-G		not specified	Uncertain significance (May 21, 2024)
11-57302166-C-T		not specified	Uncertain significance (Jan 02, 2024)
11-57302172-C-T		not specified	Uncertain significance (May 06, 2024)
11-57302221-T-G		not specified	Uncertain significance (Nov 17, 2022)
11-57302518-G-A		not specified	Uncertain significance (Jul 19, 2022)
11-57302589-G-C		not specified	Uncertain significance (Nov 14, 2023)
11-57302596-T-G		not specified	Uncertain significance (Jul 29, 2022)
11-57302616-G-A		not specified	Uncertain significance (Nov 02, 2023)
11-57302651-C-T			Likely benign (Feb 01, 2023)
11-57302689-C-G		not specified	Uncertain significance (Jan 19, 2024)
11-57302701-G-T		not specified	Uncertain significance (Dec 28, 2022)
11-57302710-G-A		not specified	Uncertain significance (Mar 26, 2024)
11-57302715-G-A		not specified	Likely benign (Apr 05, 2023)
11-57302733-C-T		not specified	Uncertain significance (Jul 08, 2022)
11-57302758-C-A		not specified	Uncertain significance (Apr 12, 2023)
11-57302759-T-A			Likely benign (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNKS1BP1	protein_coding	protein_coding	ENST00000532437	10	25315

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0826	0.917	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.157	991	977	1.01	0.0000577	11060
Missense in Polyphen		295	312.14	0.94508		3416
Synonymous	0.0432	407	408	0.997	0.0000255	3701
Loss of Function	5.48	15	61.3	0.245	0.00000313	697

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000311	0.000304
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000109	0.000109
Finnish	0.000192	0.000185
European (Non-Finnish)	0.000164	0.000158
Middle Eastern	0.000109	0.000109
South Asian	0.0000980	0.0000980
Other	0.000708	0.000652

dbNSFP

Source: dbNSFP

• Pathway: Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Metabolism of RNA;TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain;TP53 Regulates Transcription of Cell Cycle Genes;Transcriptional Regulation by TP53;Deadenylation of mRNA;Deadenylation-dependent mRNA decay (Consensus)

Recessive Scores

• pRec: 0.0984

Intolerance Scores

• loftool: 0.590
• rvis_EVS: 1.92
• rvis_percentile_EVS: 97.43

Haploinsufficiency Scores

• pHI: 0.316
• hipred: N
• hipred_score: 0.478
• ghis: 0.435

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.624

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnks1bp1

Gene ontology

• Biological process: nuclear-transcribed mRNA poly(A) tail shortening;double-strand break repair;DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest;telomere maintenance via telomerase;positive regulation of peptidyl-threonine phosphorylation;positive regulation of protein autophosphorylation;positive regulation of peptidyl-serine phosphorylation;cellular response to ionizing radiation
• Cellular component: nucleus;nuclear heterochromatin;cytoplasm;cytosol;cytoskeleton;cell-cell adherens junction;CCR4-NOT complex
• Molecular function: protein binding;enzyme binding;protein-containing complex binding;cadherin binding;ankyrin repeat binding