TNK1

tyrosine kinase non receptor 1, the group of TNK family tyrosine kinases

Basic information

Region (hg38): 17:7380534-7389774

Links

ENSG00000174292 ∙ NCBI:8711 ∙ OMIM:608076 ∙ HGNC:11940 ∙ Uniprot:Q13470 ∙ 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 TNK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TNK1 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				4	6	10
missense			43	4	5	52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)					1	1
splice region						0
non coding				1		1
Total	0	0	43	9	12

Variants in TNK1

This is a list of pathogenic ClinVar variants found in the TNK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7382947-C-T		TNK1-related disorder	Benign (Oct 17, 2019)
17-7382970-G-A		not specified	Uncertain significance (Dec 18, 2023)
17-7382970-G-C		not specified	Uncertain significance (Dec 21, 2022)
17-7383007-T-A		TNK1-related disorder	Benign (Oct 18, 2019)
17-7383024-C-T		not specified	Uncertain significance (Apr 12, 2022)
17-7383067-C-T		TNK1-related disorder	Likely benign (Aug 20, 2019)
17-7383068-G-A		not specified	Likely benign (Oct 05, 2021)
17-7383083-C-T		not specified	Uncertain significance (Jan 30, 2024)
17-7383502-G-T		not specified	Uncertain significance (Jan 10, 2023)
17-7383583-C-G		Frontotemporal dementia;Primary degenerative dementia of the Alzheimer type, presenile onset	Uncertain significance (Oct 28, 2019)
17-7383595-G-T		not specified	Uncertain significance (Feb 23, 2023)
17-7383597-C-T		not specified	Uncertain significance (Jul 13, 2021)
17-7383694-TC-T		TNK1-related disorder	Likely benign (Mar 11, 2019)
17-7383742-C-T		not specified	Uncertain significance (May 26, 2022)
17-7383817-C-T		not specified	Uncertain significance (Apr 27, 2023)
17-7383827-G-A		not specified	Uncertain significance (Mar 11, 2022)
17-7383853-C-G		not specified	Uncertain significance (Mar 04, 2024)
17-7384023-C-T		TNK1-related disorder	Likely benign (Jul 09, 2019)
17-7384030-C-T		not specified	Uncertain significance (Feb 15, 2023)
17-7384062-C-A		not specified	Uncertain significance (Mar 22, 2022)
17-7384066-C-T		not specified	Uncertain significance (May 14, 2024)
17-7384166-A-G		not specified	Uncertain significance (Jun 03, 2022)
17-7384192-C-T		not specified	Uncertain significance (Jun 10, 2024)
17-7384210-G-C		not specified	Uncertain significance (Nov 29, 2023)
17-7384219-G-A		TNK1-related disorder	Benign (Mar 20, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TNK1	protein_coding	protein_coding	ENST00000576812	12	9241

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.64e-8	0.909	109295	792	14603	124690	0.0638

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	328	383	0.856	0.0000220	4158
Missense in Polyphen		112	132.11	0.8478		1620
Synonymous	1.73	129	157	0.824	0.00000875	1464
Loss of Function	1.77	16	25.7	0.623	0.00000124	294

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.135	0.134
Ashkenazi Jewish	0.0687	0.0657
East Asian	0.180	0.165
Finnish	0.0449	0.0423
European (Non-Finnish)	0.0554	0.0509
Middle Eastern	0.180	0.165
South Asian	0.0479	0.0429
Other	0.0672	0.0643

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in negative regulation of cell growth. Has tumor suppressor properties. Plays a negative regulatory role in the Ras-MAPK pathway. May function in signaling pathways utilized broadly during fetal development and more selectively in adult tissues and in cells of the lymphohematopoietic system. Could specifically be involved in phospholipid signal transduction. {ECO:0000269|PubMed:10873601, ECO:0000269|PubMed:18974114}.
• Pathway: Focal Adhesion (Consensus)

Recessive Scores

• pRec: 0.181

Intolerance Scores

• loftool: 0.623
• rvis_EVS: 0.09
• rvis_percentile_EVS: 60.57

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.234
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.328

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tnk1
• Phenotype: respiratory system phenotype; liver/biliary system phenotype; neoplasm; digestive/alimentary phenotype; endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Gene ontology

• Biological process: protein phosphorylation;cell differentiation;negative regulation of cell growth;peptidyl-tyrosine autophosphorylation;regulation of cell population proliferation;negative regulation of Ras protein signal transduction;protein autophosphorylation
• Cellular component: cytoplasm;cytosol;membrane
• Molecular function: protein tyrosine kinase activity;non-membrane spanning protein tyrosine kinase activity;protein binding;ATP binding