CSNK2A2

casein kinase 2 alpha 2

Basic information

Region (hg38): 16:58157907-58198106

Links

ENSG00000070770 ∙ NCBI:1459 ∙ OMIM:115442 ∙ HGNC:2459 ∙ Uniprot:P19784 ∙ 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 CSNK2A2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CSNK2A2 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			7			7
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					17	17
Total	0	0	8	0	18

Variants in CSNK2A2

This is a list of pathogenic ClinVar variants found in the CSNK2A2 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-58164145-G-A		not specified	Uncertain significance (Oct 08, 2024)
16-58164235-G-C			Benign (Jun 19, 2021)
16-58165299-G-T			Benign (Nov 10, 2018)
16-58165616-C-T		not specified	Uncertain significance (Apr 25, 2023)
16-58165652-C-G		not specified	Uncertain significance (Oct 12, 2022)
16-58165665-T-C			Uncertain significance (Nov 01, 2024)
16-58165766-C-T			Benign (Nov 10, 2018)
16-58165848-G-T			Benign (Nov 11, 2018)
16-58165950-C-T			Benign (Jun 19, 2021)
16-58166599-T-C		not specified	Uncertain significance (Jun 05, 2024)
16-58166678-G-T		not specified	Uncertain significance (Nov 29, 2024)
16-58166713-A-C			Benign (Nov 12, 2018)
16-58167069-C-T			Benign (Nov 10, 2018)
16-58167277-A-C		not specified	Uncertain significance (Sep 16, 2021)
16-58167724-T-C			Benign (Jun 09, 2021)
16-58167855-A-G			Benign (Nov 10, 2018)
16-58167945-C-T			Benign (Jun 19, 2021)
16-58168027-T-C			Benign (Nov 12, 2018)
16-58174486-A-C		not specified	Uncertain significance (Jan 22, 2024)
16-58174632-T-C			Benign (Nov 12, 2018)
16-58184072-T-C			Benign (Nov 11, 2018)
16-58184585-G-A			Benign (Jun 19, 2021)
16-58186757-C-T		not specified	Uncertain significance (Dec 04, 2024)
16-58186853-C-G		not specified	Uncertain significance (Dec 28, 2023)
16-58196420-A-G			Benign (Nov 12, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CSNK2A2	protein_coding	protein_coding	ENST00000262506	11	40014

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000596	125736	0	2	125738	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.15	70	193	0.362	0.0000102	2309
Missense in Polyphen		13	81.474	0.15956		984
Synonymous	2.37	43	67.8	0.634	0.00000343	621
Loss of Function	4.53	1	25.8	0.0387	0.00000159	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000616	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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. Regulates numerous cellular processes, such as cell cycle progression, apoptosis and transcription, as well as viral infection. May act as a regulatory node which integrates and coordinates numerous signals leading to an appropriate cellular response. During mitosis, functions as a component of the p53/TP53-dependent spindle assembly checkpoint (SAC) that maintains cyclin-B-CDK1 activity and G2 arrest in response to spindle damage. Also required for p53/TP53-mediated apoptosis, phosphorylating 'Ser-392' of p53/TP53 following UV irradiation. Can also negatively regulate apoptosis. Phosphorylates the caspases CASP9 and CASP2 and the apoptotic regulator NOL3. Phosphorylation protects CASP9 from cleavage and activation by CASP8, and inhibits the dimerization of CASP2 and activation of CASP8. Regulates transcription by direct phosphorylation of RNA polymerases I, II, III and IV. Also phosphorylates and regulates numerous transcription factors including NF-kappa-B, STAT1, CREB1, IRF1, IRF2, ATF1, SRF, MAX, JUN, FOS, MYC and MYB. Phosphorylates Hsp90 and its co-chaperones FKBP4 and CDC37, which is essential for chaperone function. Regulates Wnt signaling by phosphorylating CTNNB1 and the transcription factor LEF1. Acts as an ectokinase that phosphorylates several extracellular proteins. During viral infection, phosphorylates various proteins involved in the viral life cycles of EBV, HSV, HBV, HCV, HIV, CMV and HPV. {ECO:0000269|PubMed:11239457, ECO:0000269|PubMed:11704824, ECO:0000269|PubMed:16193064}.
• 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);Allograft Rejection;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;Generic Transcription Pathway;Regulation of PTEN stability and activity;Metabolism of lipids;Metabolism of proteins;RNA Polymerase II Transcription;Chaperonin-mediated protein folding;Metabolism;Synthesis of PC;Receptor Mediated Mitophagy;Mitophagy;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;Cell Cycle, Mitotic;Intracellular signaling by second messengers;WNT mediated activation of DVL;Transcriptional regulation by RUNX1;TCF dependent signaling in response to WNT (Consensus)

Recessive Scores

• pRec: 0.586

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.996
• hipred: Y
• hipred_score: 0.819
• ghis: 0.627

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.985

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Csnk2a2
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: apoptotic process;cell cycle;spermatogenesis;Wnt signaling pathway;peptidyl-serine phosphorylation;cerebral cortex development;liver regeneration;regulation of signal transduction by p53 class mediator;regulation of autophagy of mitochondrion;positive regulation of protein targeting to mitochondrion;regulation of chromosome separation;negative regulation of ubiquitin-dependent protein catabolic process;negative regulation of apoptotic signaling pathway
• Cellular component: chromatin;acrosomal vesicle;nucleus;nucleoplasm;cytosol;plasma membrane;PcG protein complex
• Molecular function: protein serine/threonine kinase activity;protein binding;ATP binding;protein N-terminus binding