CSNK1G3

protein-coding

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

Gene summary

This gene encodes a member of a family of serine/threonine protein kinases that phosphorylate caseins and other acidic proteins. A related protein in the African clawed frog participates in the transmission of Wnt/beta-catenin signaling. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

MANE transcript

NM_001364140.2

Inheritance

—

ClinVar variants

U:38B:2

Top phenotype

CSNK1G3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr5:123,512,177-123,617,049

External References & Databases

Ensembl (ENSG00000151292)

Transcript & Mutation Effects

hg38 • Region Span ~104.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Tourette syndromeLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0007661

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CSNK1G3 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 31

CSNK1G3-related disorderTotal: 4

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001364140.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			3 clinvar	2 clinvar		5
missense			32 clinvar			32
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	38	2	0	40

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 158 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001364140.2	RefSeq	NP_001351069.1	13	MANE Select
ENST00000696905.1	Ensembl	ENSP00000512966.1	13	MANE Select
NM_001031812.4	RefSeq	NP_001026982.1	12	Standard
NM_001044723.3	RefSeq	NP_001038188.1	13	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Hedgehog signaling pathway - Homo sapiens (human)
Hedgehog Signaling Pathway
IL-7 signaling
JAK STAT pathway and regulation
EPO signaling

Biological Process

cellular protein modification process
endocytosis
signal transduction
Wnt signaling pathway
peptidyl-serine phosphorylation

Molecular Function

protein kinase activity
protein serine/threonine kinase activity
ATP binding

Cellular Component

nucleus
cytoplasm
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000395412
Coding exons: 13
Length: 104947
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 9
Defined: 125721
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.75	121	241	0.502	0.0000119	2976
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0	0.0	absent
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.181

Intolerance Scores

LoFtool: 0.459
RVIS EVS: -0.32
RVIS percentile EVS: 31.46

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.973

Gene Damage Prediction

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