CSNK1G1

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

Basic information

Region (hg38): 15:64165525-64356173

Links

ENSG00000169118 ∙ NCBI:53944 ∙ OMIM:606274 ∙ HGNC:2454 ∙ Uniprot:Q9HCP0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSNK1G1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSNK1G1 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		1
missense			21	1		22
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	2	0

Variants in CSNK1G1

This is a list of pathogenic ClinVar variants found in the CSNK1G1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-64171941-C-T		not specified	Uncertain significance (Jan 29, 2024)
15-64180373-C-T		not specified	Uncertain significance (Feb 28, 2023)
15-64180453-A-G		not specified	Uncertain significance (Mar 06, 2023)
15-64180454-C-T		not specified	Uncertain significance (Jan 22, 2024)
15-64203089-C-T		not specified	Uncertain significance (Mar 06, 2023)
15-64203144-T-C		not specified	Uncertain significance (Feb 16, 2023)
15-64204455-C-T			Likely benign (Feb 01, 2023)
15-64204509-A-G		not specified	Uncertain significance (Jan 24, 2024)
15-64204948-G-C		not specified	Uncertain significance (Mar 07, 2024)
15-64207586-G-A			Uncertain significance (Jun 15, 2014)
15-64213982-T-C			Uncertain significance (Jun 09, 2022)
15-64214016-T-C		not specified	Uncertain significance (Jun 01, 2023)
15-64214048-C-G		not specified	Uncertain significance (Dec 31, 2023)
15-64214049-G-A			Uncertain significance (Nov 01, 2021)
15-64214054-A-G		not specified	Uncertain significance (Aug 02, 2021)
15-64214081-C-A			Uncertain significance (Jul 08, 2020)
15-64216566-T-C		not specified	Uncertain significance (Jun 01, 2023)
15-64216638-G-C		See cases	Uncertain significance (Feb 05, 2021)
15-64216692-T-C		not specified	Uncertain significance (Jul 26, 2022)
15-64259217-T-C		not specified	Uncertain significance (Apr 09, 2024)
15-64259223-T-C		not specified	Uncertain significance (Jan 09, 2024)
15-64259233-G-A		not specified	Uncertain significance (Feb 27, 2023)
15-64300404-T-C			Likely benign (Feb 01, 2024)
15-64300420-C-T		not specified	Uncertain significance (May 09, 2023)
15-64300421-G-C		not specified	Uncertain significance (Nov 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSNK1G1	protein_coding	protein_coding	ENST00000303052	11	190727

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000893	125736	0	8	125744	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.99	151	237	0.636	0.0000127	2756
Missense in Polyphen		58	111.26	0.52128		1281
Synonymous	0.224	80	82.6	0.969	0.00000437	787
Loss of Function	4.66	2	29.1	0.0686	0.00000197	300

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000176	0.0000176
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

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). Phosphorylates CLSPN. {ECO:0000250, ECO:0000269|PubMed:21680713}.
• Pathway: Hedgehog signaling pathway - Homo sapiens (human);WNT-Core;Wnt Signaling Pathway;Hedgehog Signaling Pathway;IL-7 signaling;JAK STAT pathway and regulation;EPO signaling;VEGF;Canonical Wnt signaling pathway;FoxO family signaling;Hedgehog signaling events mediated by Gli proteins;p53 pathway (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.457
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.37

Haploinsufficiency Scores

• pHI: 0.466
• hipred: Y
• hipred_score: 0.534
• ghis: 0.668

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.938

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csnk1g1

Gene ontology

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