CSNK1A1

protein-coding

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

Gene summary

Enables protein serine/threonine kinase activity. Involved in several processes, including intermediate filament cytoskeleton organization; positive regulation of proteasomal ubiquitin-dependent protein catabolic process; and regulation of signal transduction. Located in cytoskeleton; cytosol; and nucleus. Part of beta-catenin destruction complex. Biomarker of Alzheimer's disease and inclusion body myositis. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001892.6

Inheritance

—

ClinVar variants

U:11

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.05

Max pathogenic AF

—

Genomic locus

chr5:149,492,982-149,551,471

External References & Databases

Ensembl (ENSG00000113712)

Transcript & Mutation Effects

hg38 • Region Span ~58.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CSNK1A1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 4

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001892.6. 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			1 clinvar			1
missense			6 clinvar			6
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	11	0	0	11

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 82 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001892.6	RefSeq	NP_001883.4	10	MANE Select
ENST00000377843.8	Ensembl	ENSP00000367074.2	10	MANE Select
NM_001025105.3	RefSeq	NP_001020276.1	11	Standard
NM_001271741.2	RefSeq	NP_001258670.1	10	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
csnk1a1	Danio rerio	Structure: cartilage element Quality: wrinkled abnormal

Gene / Model

Organism

Observed Phenotype

csnk1a1

Danio rerio

Structure: cartilage element

Quality: wrinkled

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

Biological Process

cell morphogenesis
protein phosphorylation
Golgi organization
cell cycle
signal transduction

Molecular Function

protein kinase activity
protein serine/threonine kinase activity
protein binding
ATP binding
kinase activity

Cellular Component

condensed chromosome kinetochore
nucleus
cytoplasm
centrosome
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000515768
Coding exons: 11
Length: 59248
Individuals with no LoFs: 125242
Homozygous LoFs: 0
Heterozygous LoFs: 1
Defined: 125243
p: 0.00000399

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	4.30	28	199	0.141	0.00000970	2426
Missense (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

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	0.0	absent
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

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}.;

Recessive Scores

pRec: 0.130

Intolerance Scores

RVIS EVS: -0.05
RVIS percentile EVS: 49.39

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.929