TLK1

tousled like kinase 1

Basic information

Region (hg38): 2:170990823-171231314

Links

ENSG00000198586 ∙ NCBI:9874 ∙ OMIM:608438 ∙ HGNC:11841 ∙ Uniprot:Q9UKI8 ∙ 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 TLK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TLK1 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			12			12
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in TLK1

This is a list of pathogenic ClinVar variants found in the TLK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-170993806-G-C		not specified	Uncertain significance (Apr 01, 2024)
2-170993865-C-T		not specified	Uncertain significance (Sep 14, 2022)
2-170997738-A-T		not specified	Uncertain significance (May 23, 2024)
2-171007038-T-C		not specified	Uncertain significance (Oct 06, 2021)
2-171007045-G-C		Neurodevelopmental disorder	Uncertain significance (Sep 12, 2023)
2-171014883-C-G		not specified	Uncertain significance (Sep 20, 2023)
2-171014906-C-T		not specified	Uncertain significance (Jul 09, 2021)
2-171049899-G-A		not specified	Uncertain significance (Nov 22, 2023)
2-171050140-T-C		not specified	Uncertain significance (Dec 22, 2023)
2-171050155-C-T		not specified	Uncertain significance (Dec 16, 2023)
2-171055099-G-A		not specified	Uncertain significance (Mar 01, 2024)
2-171056538-A-G		not specified	Uncertain significance (Dec 22, 2023)
2-171061128-G-C		not specified	Uncertain significance (Jul 09, 2021)
2-171117850-C-T		not specified	Uncertain significance (Dec 27, 2023)
2-171160301-C-G		not specified	Uncertain significance (Jun 17, 2024)
2-171160315-CGT-C		See cases	Uncertain significance (Jan 28, 2022)
2-171160352-C-G		not specified	Uncertain significance (Apr 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TLK1	protein_coding	protein_coding	ENST00000431350	21	240492

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.00000584	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.56	200	401	0.499	0.0000202	5034
Missense in Polyphen		47	158.8	0.29598		2030
Synonymous	0.439	133	140	0.953	0.00000691	1386
Loss of Function	5.95	3	47.0	0.0638	0.00000244	587

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000295	0.0000295
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000273	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000695	0.0000653
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Rapidly and transiently inhibited by phosphorylation following the generation of DNA double-stranded breaks during S- phase. This is cell cycle checkpoint and ATM-pathway dependent and appears to regulate processes involved in chromatin assembly. Isoform 3 phosphorylates and enhances the stability of the t-SNARE SNAP23, augmenting its assembly with syntaxin. Isoform 3 protects the cells from the ionizing radiation by facilitating the repair of DSBs. In vitro, phosphorylates histone H3 at 'Ser-10'. {ECO:0000269|PubMed:10523312, ECO:0000269|PubMed:10588641, ECO:0000269|PubMed:11314006, ECO:0000269|PubMed:11470414, ECO:0000269|PubMed:12660173, ECO:0000269|PubMed:9427565}.
• Pathway: miRNA Regulation of DNA Damage Response;Pathways Affected in Adenoid Cystic Carcinoma;DNA Damage Response (Consensus)

Recessive Scores

• pRec: 0.117

Intolerance Scores

• loftool: 0.0789
• rvis_EVS: -0.4
• rvis_percentile_EVS: 26.53

Haploinsufficiency Scores

• pHI: 0.389
• hipred: Y
• hipred_score: 0.816
• ghis: 0.674

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.827

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tlk1

Gene ontology

• Biological process: regulation of chromatin assembly or disassembly;chromatin organization;protein phosphorylation;intracellular protein transport;cellular response to DNA damage stimulus;cell cycle;intracellular signal transduction
• Cellular component: nucleus
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding