CSNK1G3

casein kinase 1 gamma 3, the group of casein kinase 1 family

Basic information

Region (hg38): 5:123512177-123617049

Links

ENSG00000151292 ∙ NCBI:1456 ∙ OMIM:604253 ∙ HGNC:2456 ∙ Uniprot:Q9Y6M4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSNK1G3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSNK1G3 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				2		2
missense			12			12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	0	12	2	0

Variants in CSNK1G3

This is a list of pathogenic ClinVar variants found in the CSNK1G3 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-123545680-A-G		not specified	Uncertain significance (Jan 02, 2024)
5-123545728-C-T		not specified	Uncertain significance (Sep 11, 2024)
5-123545797-T-C		not specified	Uncertain significance (May 06, 2024)
5-123553121-A-T		not specified	Uncertain significance (Aug 21, 2023)
5-123573408-T-C		not specified	Uncertain significance (Jan 23, 2024)
5-123573438-A-G		not specified	Uncertain significance (Aug 13, 2021)
5-123573501-C-T		not specified	Uncertain significance (Aug 13, 2021)
5-123575736-G-A		not specified	Uncertain significance (Apr 01, 2024)
5-123575872-T-A		not specified	Uncertain significance (Jun 07, 2024)
5-123575874-C-T		not specified	Uncertain significance (Feb 09, 2022)
5-123588472-C-T		not specified	Uncertain significance (Nov 30, 2022)
5-123590472-G-C		not specified	Uncertain significance (Mar 25, 2024)
5-123590505-G-A		not specified	Uncertain significance (Jan 31, 2022)
5-123591335-C-G		not specified	Uncertain significance (Oct 25, 2022)
5-123591374-C-G		not specified	Uncertain significance (Dec 21, 2022)
5-123595128-G-A		CSNK1G3-related disorder	Likely benign (Aug 30, 2019)
5-123604718-A-G		CSNK1G3-related disorder	Benign (Mar 25, 2019)
5-123604720-A-G		CSNK1G3-related disorder	Likely benign (Mar 11, 2019)
5-123604724-G-T		not specified	Uncertain significance (Mar 02, 2023)
5-123604734-C-T		not specified	Uncertain significance (Oct 22, 2021)
5-123614349-T-C		not specified	Uncertain significance (Sep 02, 2024)
5-123614378-C-T		CSNK1G3-related disorder	Likely benign (Dec 09, 2019)
5-123614379-A-G		not specified	Uncertain significance (Aug 11, 2024)
5-123614385-C-T		not specified	Uncertain significance (Oct 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSNK1G3	protein_coding	protein_coding	ENST00000395412	13	104947

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000526	125712	0	9	125721	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.75	121	241	0.502	0.0000119	2976
Missense in Polyphen		21	83.506	0.25148		1096
Synonymous	0.170	77	78.9	0.976	0.00000392	806
Loss of Function	4.79	2	30.6	0.0655	0.00000178	369

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000548	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000622	0.0000616
Middle Eastern	0.0000548	0.0000544
South Asian	0.00	0.00
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Serine/threonine-protein kinase. 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. Regulates fast synaptic transmission mediated by glutamate (By similarity). {ECO:0000250}.
• Pathway: Hedgehog signaling pathway - Homo sapiens (human);Hedgehog Signaling Pathway;IL-7 signaling;JAK STAT pathway and regulation;EPO signaling;VEGF;FoxO family signaling;Hedgehog signaling events mediated by Gli proteins;p53 pathway (Consensus)

Recessive Scores

• pRec: 0.181

Intolerance Scores

• loftool: 0.459
• rvis_EVS: -0.32
• rvis_percentile_EVS: 31.46

Haploinsufficiency Scores

• pHI: 0.426
• hipred: Y
• hipred_score: 0.662
• ghis: 0.693

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.973

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csnk1g3
• Phenotype: hematopoietic system phenotype; skeleton phenotype; immune system phenotype; craniofacial phenotype

Gene ontology

• Biological process: cellular protein modification process;endocytosis;signal transduction;Wnt signaling pathway;peptidyl-serine phosphorylation;peptidyl-threonine phosphorylation;positive regulation of canonical Wnt signaling pathway
• Cellular component: nucleus;cytoplasm;plasma membrane
• Molecular function: protein kinase activity;protein serine/threonine kinase activity;ATP binding