CSNK1E

casein kinase 1 epsilon, the group of casein kinase 1 family

Basic information

Region (hg38): 22:38290691-38318084

Links

ENSG00000213923

∙ NCBI:1454 ∙ OMIM:600863 ∙ HGNC:2453 ∙ Uniprot:P49674 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

developmental and epileptic encephalopathy (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSNK1E gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSNK1E 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					1 clinvar	1
missense			12 clinvar			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1 clinvar	1
Total	0	0	12	0	2

Variants in CSNK1E

This is a list of pathogenic ClinVar variants found in the CSNK1E region.

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

Position	Phenotype	Significance	ClinVar
22-38294141-G-A	not specified	Uncertain significance (Sep 20, 2023)	3078275
22-38294158-G-A	not specified	Uncertain significance (Feb 27, 2024)	3078274
22-38294176-G-A	not specified	Uncertain significance (Jul 13, 2021)	2231341
22-38294256-G-T		Benign (Jul 06, 2018)	724802
22-38294347-G-A	not specified	Uncertain significance (Aug 17, 2022)	2377384
22-38294368-G-A	not specified	Uncertain significance (Nov 19, 2022)	2328246
22-38294393-T-C	not specified	Uncertain significance (Aug 14, 2023)	2588640
22-38294408-C-T	not specified	Uncertain significance (Jun 07, 2024)	3269883
22-38294443-C-T	not specified	Uncertain significance (Aug 19, 2021)	2213495
22-38294458-C-T	not specified	Uncertain significance (Jul 05, 2023)	2594796
22-38294506-T-C	not specified	Uncertain significance (Feb 09, 2023)	2482498
22-38298785-C-T	Developmental and epileptic encephalopathy, 1	Pathogenic (-)	590290
22-38300757-G-A	12 conditions	Uncertain significance (Jun 20, 2023)	2570671
22-38300896-G-A		Benign (Dec 31, 2019)	789683
22-38302851-G-A		Benign (Oct 09, 2018)	724803
22-38302910-C-A		Uncertain significance (Mar 17, 2020)	929456
22-38314121-G-A		Uncertain significance (Sep 01, 2022)	2653138

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSNK1E	protein_coding	protein_coding	ENST00000396832	9	107831

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000742	125742	0	3	125745	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.18	136	288	0.472	0.0000209	2688
Missense in Polyphen		57	127.52	0.44698		1149
Synonymous	0.242	116	119	0.972	0.00000869	828
Loss of Function	4.23	0	20.8	0.00	0.00000112	224

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)	0.0000354	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Casein kinases are operationally defined by their preferential utilization of acidic proteins such as caseins as substrates. Can phosphorylate a large number of proteins. Participates in Wnt signaling. Phosphorylates DVL1 and DVL2. Central component of the circadian clock. In balance with PP1, determines the circadian period length, through the regulation of the speed and rhythmicity of PER1 and PER2 phosphorylation. Controls PER1 and PER2 nuclear transport and degradation. Inhibits cytokine-induced granuloytic differentiation. {ECO:0000269|PubMed:12556519, ECO:0000269|PubMed:15070676, ECO:0000269|PubMed:15917222, ECO:0000269|PubMed:16790549, ECO:0000269|PubMed:23413191}.;
Pathway: Circadian rhythm - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);Hippo signaling pathway - Homo sapiens (human);Hippo signaling pathway - multiple species - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);Hedgehog signaling pathway - Homo sapiens (human);Melatonin metabolism and effects;Wnt Signaling Pathway;Wnt Signaling Pathway and Pluripotency;Hedgehog Signaling Pathway;Wnt Signaling Pathway;Signaling by WNT;Signal Transduction;Circadian Clock;IL-7 signaling;Regulation of PLK1 Activity at G2/M Transition;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;JAK STAT pathway and regulation;EPO signaling;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Wnt;VEGF;Cell Cycle, Mitotic;Circadian rhythm pathway;Anchoring of the basal body to the plasma membrane;Wnt Canonical;WNT mediated activation of DVL;Degradation of beta catenin;TCF dependent signaling in response to WNT;FoxO family signaling;Wnt Mammals;Hedgehog signaling events mediated by Gli proteins;p53 pathway;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

pRec: 0.586

Intolerance Scores

loftool: 0.348
rvis_EVS: -0.34
rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

pHI: 0.931
hipred: Y
hipred_score: 0.825
ghis: 0.620

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.959

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Csnk1e
Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan);

Gene ontology

Biological process: G2/M transition of mitotic cell cycle;DNA repair;protein phosphorylation;endocytosis;signal transduction;regulation of G2/M transition of mitotic cell cycle;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;negative regulation of protein binding;positive regulation of proteasomal ubiquitin-dependent protein catabolic process;circadian regulation of gene expression;regulation of circadian rhythm;canonical Wnt signaling pathway;positive regulation of canonical Wnt signaling pathway;ciliary basal body-plasma membrane docking;regulation of cellular protein localization;positive regulation of Wnt-mediated midbrain dopaminergic neuron differentiation;positive regulation of non-canonical Wnt signaling pathway
Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol
Molecular function: RNA binding;protein kinase activity;protein serine/threonine kinase activity;protein binding;ATP binding