CSNK1A1L
Basic information
Region (hg38): 13:37103259-37105664
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSNK1A1L 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 | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 13 | 0 | 0 |
Variants in CSNK1A1L
This is a list of pathogenic ClinVar variants found in the CSNK1A1L region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 13-37104256-A-C | not specified | Uncertain significance (Dec 31, 2023) | ||
| 13-37104338-G-C | not specified | Uncertain significance (Sep 29, 2023) | ||
| 13-37104412-C-T | not specified | Uncertain significance (Sep 26, 2023) | ||
| 13-37104583-C-G | not specified | Uncertain significance (Jul 14, 2021) | ||
| 13-37104604-C-T | not specified | Uncertain significance (May 14, 2024) | ||
| 13-37104716-G-A | not specified | Uncertain significance (Feb 10, 2022) | ||
| 13-37104913-A-C | not specified | Uncertain significance (Oct 27, 2022) | ||
| 13-37105016-G-T | not specified | Uncertain significance (Aug 11, 2022) | ||
| 13-37105028-G-A | not specified | Uncertain significance (Feb 23, 2023) | ||
| 13-37105099-T-G | not specified | Uncertain significance (Nov 03, 2023) | ||
| 13-37105151-T-C | not specified | Uncertain significance (Mar 08, 2024) | ||
| 13-37105195-C-T | not specified | Uncertain significance (Jun 16, 2023) | ||
| 13-37105214-C-T | not specified | Uncertain significance (Mar 24, 2023) | ||
| 13-37105244-T-A | not specified | Uncertain significance (Dec 18, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CSNK1A1L | protein_coding | protein_coding | ENST00000379800 | 1 | 2406 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0132 | 0.872 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.172 | 178 | 185 | 0.964 | 0.0000111 | 2248 |
| Missense in Polyphen | 73 | 75.343 | 0.9689 | 988 | ||
| Synonymous | -1.09 | 84 | 72.2 | 1.16 | 0.00000470 | 624 |
| Loss of Function | 1.31 | 4 | 7.98 | 0.501 | 6.29e-7 | 94 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. It can phosphorylate a large number of proteins. Participates in Wnt signaling (By similarity). {ECO:0000250}.;
- Pathway
- Gastric cancer - Homo sapiens (human);Breast cancer - Homo sapiens (human);Hepatocellular carcinoma - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Human papillomavirus infection - Homo sapiens (human);Hedgehog signaling pathway - Homo sapiens (human);WNT-Core;HH-Core;Chromosomal and microsatellite instability in colorectal cancer;Hedgehog Signaling Pathway;Wnt Signaling Pathway
(Consensus)
Recessive Scores
- pRec
- 0.171
Intolerance Scores
- loftool
- 0.908
- rvis_EVS
- 0.55
- rvis_percentile_EVS
- 81.48
Haploinsufficiency Scores
- pHI
- 0.0957
- hipred
- N
- hipred_score
- 0.168
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.914
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- Wnt signaling pathway;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;negative regulation of canonical Wnt signaling pathway
- Cellular component
- nucleus;cytoplasm;cytosol
- Molecular function
- protein serine/threonine kinase activity;ATP binding