CSNK1A1
casein kinase 1 alpha 1, the group of casein kinase 1 family
Basic information
Region (hg38): 5:149492982-149551471
Links
Phenotypes
GenCC
Source:
No genCC data.
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 CSNK1A1 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 | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 3 | 0 | 0 |
Variants in CSNK1A1
This is a list of pathogenic ClinVar variants found in the CSNK1A1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-149495744-TAAAA-T | CIC-rearranged sarcoma | not provided (-) | ||
| 5-149505465-T-A | not specified | Uncertain significance (Mar 30, 2024) | ||
| 5-149505494-T-A | not specified | Uncertain significance (Dec 04, 2024) | ||
| 5-149505506-C-T | not specified | Uncertain significance (Dec 27, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CSNK1A1 | protein_coding | protein_coding | ENST00000515768 | 11 | 59248 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.998 | 0.00242 | 125242 | 0 | 1 | 125243 | 0.00000399 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 4.30 | 28 | 199 | 0.141 | 0.00000970 | 2426 |
| Missense in Polyphen | 3 | 66.407 | 0.045176 | 858 | ||
| Synonymous | 0.302 | 65 | 68.2 | 0.953 | 0.00000319 | 645 |
| Loss of Function | 4.15 | 1 | 22.1 | 0.0453 | 0.00000110 | 275 |
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 | 0.0000462 | 0.0000462 |
| 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. Phosphorylates CTNNB1 at 'Ser-45'. May phosphorylate PER1 and PER2. May play a role in segregating chromosomes during mitosis (PubMed:11955436, PubMed:1409656, PubMed:18305108). May play a role in keratin cytoskeleton disassembly and thereby, it may regulate epithelial cell migration (PubMed:23902688). {ECO:0000269|PubMed:11955436, ECO:0000269|PubMed:1409656, ECO:0000269|PubMed:18305108, ECO:0000269|PubMed:23902688}.;
- 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);T-Cell Receptor and Co-stimulatory Signaling;Human Complement System;Wnt Signaling Pathway;Wnt-beta-catenin Signaling Pathway in Leukemia;Regulation of Wnt-B-catenin Signaling by Small Molecule Compounds;Chromosomal and microsatellite instability in colorectal cancer;Hedgehog Signaling Pathway;Wnt Signaling Pathway;Degradation of beta-catenin by the destruction complex;Signaling by WNT;Signal Transduction;GLI3 is processed to GLI3R by the proteasome;Activation of SMO;Disassembly of the destruction complex and recruitment of AXIN to the membrane;Degradation of GLI2 by the proteasome;Hedgehog ,off, state;IL-7 signaling;Hedgehog ,on, state;Signaling by Hedgehog;JAK STAT pathway and regulation;Noncanonical Wnt signaling pathway;EPO signaling;Beta-catenin phosphorylation cascade;Wnt;VEGF;Degradation of beta catenin;TCF dependent signaling in response to WNT;FoxO family signaling;Role of Calcineurin-dependent NFAT signaling in lymphocytes;Hedgehog signaling events mediated by Gli proteins;Presenilin action in Notch and Wnt signaling;p53 pathway
(Consensus)
Recessive Scores
- pRec
- 0.130
Intolerance Scores
- loftool
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.39
Haploinsufficiency Scores
- pHI
- 0.623
- hipred
- Y
- hipred_score
- 0.681
- ghis
- 0.607
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.929
Mouse Genome Informatics
- Gene name
- Csnk1a1
- Phenotype
- digestive/alimentary phenotype; hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; immune system phenotype; liver/biliary system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); pigmentation phenotype; neoplasm; craniofacial phenotype; cellular phenotype; growth/size/body region 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);
Zebrafish Information Network
- Gene name
- csnk1a1
- Affected structure
- cartilage element
- Phenotype tag
- abnormal
- Phenotype quality
- wrinkled
Gene ontology
- Biological process
- cell morphogenesis;protein phosphorylation;Golgi organization;cell cycle;signal transduction;cell surface receptor signaling pathway;Wnt signaling pathway;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;intermediate filament cytoskeleton organization;cell division;negative regulation of canonical Wnt signaling pathway;regulation of GTP binding;beta-catenin destruction complex assembly;beta-catenin destruction complex disassembly
- Cellular component
- condensed chromosome kinetochore;nucleus;cytoplasm;centrosome;cytosol;mRNA cleavage and polyadenylation specificity factor complex;cilium;membrane;nuclear speck;beta-catenin destruction complex;ciliary basal body;keratin filament;ribonucleoprotein complex
- Molecular function
- protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding;kinase activity