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Gene

CSNK2A1

casein kinase 2 alpha 1

Summary

Cytogenetic location
20p13
Coordinates
Chromosome 20: 472,498–543,790 (GRCh38)
Exons
14 exons across 71.3 kb
Protein
391 amino acids
Also known as
Cka1, Cka2
MANE Select transcript
ENST00000217244.9NM_177559.3
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated report relevant to this gene

    • Intellectual Disability

      • One of 233 genes linked to it

        • ClinGen rates the link definitive
        • 1 GenCC submitter rates it definitive or strong

    How CSNK2A1 is laid out

    • Coding sequence
    • Untranslated region
    • Intron
    • Direction of transcription
    • Known disease-causing sites
    • Stretches short reads find hard
    Chromosome 20, with a bracket where CSNK2A1 sits. CSNK2A1 and 21 genes near it on chromosome 20, from 8,144 to 1,008,143.Chromosome 2020p13p13p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11.1q11.21q11.22q11.23q12q13.11q13.12q13.13q13.2q13.31q13.32q13.330.2 Mb0.4 Mb0.6 Mb0.8 Mb1 MbDEFB125: 87,250–97,094, forward strandDEFB125DEFB126: 142,590–145,751, forward strandDEFB126DEFB127: 157,454–159,163, forward strandDEFB127DEFB128: 187,853–189,711, reverse strandDEFB128DEFB129: 227,258–229,886, forward strandDEFB129DEFB132: 257,717–261,096, forward strandDEFB132C20orf96: 270,863–290,778, reverse strandC20orf96ZCCHC3: 297,570–300,321, forward strandZCCHC3SOX12: 325,552–330,224, forward strandSOX12NRSN2: 346,695–359,706, forward strandNRSN2TRIB3: 362,835–398,964, forward strandTRIB3RBCK1: 407,393–432,139, forward strandRBCK1TBC1D20: 423,596–462,566, reverse strandTBC1D20CSNK2A1: 472,498–543,790, reverse strandCSNK2A1TCF15: 603,801–610,316, reverse strandTCF15SRXN1: 646,614–653,404, reverse strandSRXN1: 646,626–675,800, reverse strandSCRT2: 661,596–675,802, reverse strandSCRT2SLC52A3: 758,695–776,015, reverse strandSLC52A3FAM110A: 833,707–857,463, forward strandFAM110AANGPT4: 869,900–916,335, reverse strandANGPT4RSPO4: 958,452–1,002,510, reverse strandRSPO4Diagram of CSNK2A1: 14 exons on the reverse strand of chromosome 20Exon 12: 8 known disease-causing sitesExon 10: 3 known disease-causing sitesExon 9: 12 known disease-causing sitesExon 8: 6 known disease-causing sitesExon 7: 2 known disease-causing sitesExon 6: 1 known disease-causing siteExon 5: 3 known disease-causing sitesExon 4: 11 known disease-causing sitesExon 3: 1 known disease-causing siteExon 14: 472,498–484,076, 11,579 basesExon 13: 486,376–486,462, 87 basesExon 12: 487,427–487,575, 149 basesExon 11: 488,678–488,778, 101 basesExon 10: 489,780–489,881, 102 basesExon 9: 492,254–492,364, 111 basesExon 8: 495,719–495,802, 84 basesExon 7: 497,721–497,780, 60 basesExon 6: 499,255–499,305, 51 basesExon 5: 499,833–499,934, 102 basesExon 4: 505,118–505,229, 112 basesExon 3: 508,451–508,660, 210 basesExon 2: 527,933–528,049, 117 basesExon 1: 543,672–543,790, 119 bases141210864215′3′

    Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

    Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

    Nearby genes from Ensembl release 116, on GRCh38.

    Exons make up 13 kb of the gene's 71.3 kb; 1,176 of those bases code for the protein.

    How a genome test reads CSNK2A1

    49

    positions in CSNK2A1 where ClinVar classes a change as pathogenic or likely pathogenic

    5 of them (10%) fall in regions short reads find hard.

    • Low mappability (5 sites)Regions where 100 bp or 250 bp reads cannot be placed uniquely.

    A whole genome covers all 71.3 kb of CSNK2A1, introns included, not only the 13 kb of exons.

    Where this comes from

    • HGNC: the gene's symbol, name, other symbols and location.
    • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
    • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
    • The ACMG secondary findings list, SF v3.2.
    • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
    • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
    • Data release 2026.10.16-c6eea6bf.

    Cite this page

    APA

    Dante Labs. (n.d.). CSNK2A1 gene: casein kinase 2 alpha 1. Retrieved 17 October 2026, from https://dantelabs.com/genes/csnk2a1

    Vancouver

    Dante Labs. CSNK2A1 gene: casein kinase 2 alpha 1 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/csnk2a1

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