CSNK2A3

casein kinase 2 alpha 3

Basic information

Region (hg38): 11:11351941-11353250

Previous symbols: [ "CSNK2A1P" ]

Links

ENSG00000254598 ∙ NCBI:283106 ∙ ∙ HGNC:2458 ∙ Uniprot:Q8NEV1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CSNK2A3 gene.

• Okur-Chung neurodevelopmental syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSNK2A3 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						0
missense		1				1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	0	0	0

Variants in CSNK2A3

This is a list of pathogenic ClinVar variants found in the CSNK2A3 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-11352540-A-G		Okur-Chung neurodevelopmental syndrome	Likely pathogenic (Feb 01, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSNK2A3	protein_coding	protein_coding	ENST00000528848	1	1416

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.10e-10	0.0373	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.629	236	210	1.12	0.0000121	2545
Missense in Polyphen		96	78.041	1.2301		999
Synonymous	0.432	74	78.9	0.938	0.00000449	758
Loss of Function	-0.396	14	12.5	1.12	0.00000122	113

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)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable catalytic subunit of a constitutively active serine/threonine-protein kinase complex that phosphorylates a large number of substrates containing acidic residues C-terminal to the phosphorylated serine or threonine. Amplification-dependent oncogene; promotes cell proliferation and tumorigenesis by down- regulating expression of the tumor suppressor protein, PML. May play a role in the pathogenesis of the lung cancer development and progression. {ECO:0000269|PubMed:20625391}.
• Pathway: Adherens junction - Homo sapiens (human);Ribosome biogenesis in eukaryotes - Homo sapiens (human);Mitophagy - animal - Homo sapiens (human);Measles - Homo sapiens (human);Wnt signaling pathway - Homo sapiens (human);NF-kappa B signaling pathway - Homo sapiens (human);Epstein-Barr virus infection - Homo sapiens (human);Herpes simplex infection - Homo sapiens (human);nerve growth factor pathway (ngf);Wnt Signaling Pathway;Developmental Biology;Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding;Signaling by WNT;Signal Transduction;Gene expression (Transcription);RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known;wnt signaling pathway;lissencephaly gene (lis1) in neuronal migration and development;segmentation clock;multi-step regulation of transcription by pitx2;bcr signaling pathway;calcium signaling by hbx of hepatitis b virus;Generic Transcription Pathway;Regulation of PTEN stability and activity;Metabolism of lipids;Metabolism of proteins;igf-1 signaling pathway;RNA Polymerase II Transcription;Chaperonin-mediated protein folding;Metabolism;Fibroblast growth factor-1;inactivation of gsk3 by akt causes accumulation of b-catenin in alveolar macrophages;Synthesis of PC;Receptor Mediated Mitophagy;Mitophagy;pdgf signaling pathway;tpo signaling pathway;BCR signaling pathway;PTEN Regulation;PIP3 activates AKT signaling;Protein folding;Regulation of TP53 Activity through Phosphorylation;Condensation of Prometaphase Chromosomes;Signal transduction by L1;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Mitotic Prometaphase;L1CAM interactions;Glycerophospholipid biosynthesis;Phospholipid metabolism;Axon guidance;M Phase;Cell Cycle;TNFalpha;Cell Cycle, Mitotic;Intracellular signaling by second messengers;WNT mediated activation of DVL;Transcriptional regulation by RUNX1;TCF dependent signaling in response to WNT;Alpha-synuclein signaling;Role of Calcineurin-dependent NFAT signaling in lymphocytes;Lissencephaly gene (LIS1) in neuronal migration and development;Presenilin action in Notch and Wnt signaling;PDGFR-alpha signaling pathway (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N

Gene Damage Prediction

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

Gene ontology

• Biological process: protein phosphorylation;positive regulation of cell population proliferation;positive regulation of cell growth;positive regulation of protein catabolic process
• Cellular component: nucleoplasm
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding