TLK1
Basic information
Region (hg38): 2:170990823-171231314
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (35 variants)
- not_provided (1 variants)
- Neurodevelopmental_disorder (1 variants)
- See_cases (1 variants)
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. These statistics are base on transcript: NM_000012290.5. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 35 | 35 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 36 | 1 | 0 |
GnomAD
Source:
| 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:
- 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
- Phenotype
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