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Gene

SKIC2

SKI2 subunit of superkiller complex

Summary

Cytogenetic location
6p21.33
Coordinates
Chromosome 6: 31,959,175–31,969,751 (GRCh38)
Exons
28 exons across 10.6 kb
Protein
1,246 amino acids
Inheritance
Autosomal dominant
Also known as
HLP, DDX13, SKI2W, 170A, SKIV2L1, SKI2
Previous symbols
SKIV2, SKIV2L
MANE Select transcript
ENST00000375394.7NM_006929.5
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 reports relevant to this gene

  • Rare Monogenic Autoinflammatory Diseases

    • PTPN2-related autoinflammation and autoimmunityAutosomal dominant

      Early-onset inflammatory and autoimmune disease, including colitis and arthritis, caused by variants in PTPN2.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong

Broader groupings

  • Other Inborn Errors of Immunity

    • Inborn error of immunity

      One of 114 genes linked to it

      Inherited disorders of the immune system caused by changes in single genes, affecting how the body fights infection or regulates inflammation.

      • ClinGen rates the link definitive
      • 4 GenCC submitters rate it definitive or strong

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How SKIC2 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
Chromosome 6, with a bracket where SKIC2 sits. SKIC2 and 70 genes near it on chromosome 6, from 31,464,463 to 32,464,462.Chromosome 66p21.33p25.3p25.2p25.1p24.3p24.2p24.1p23p22.3p22.2p22.1p21.33p21.32p21.31p21.2p21.1p12.3p12.2p12.1p11.2p11.1q11.1q11.2q12q13q14.1q14.2q14.3q15q16.1q16.2q16.3q21q22.1q22.2q22.31q22.32q22.33q23.1q23.2q23.3q24.1q24.2q24.3q25.1q25.2q25.3q26q2731.6 Mb31.8 Mb32 Mb32.2 Mb32.4 MbMICB: 31,494,881–31,511,124, forward strandMICBMCCD1: 31,528,962–31,530,232, forward strandDDX39B: 31,530,217–31,542,451, reverse strandDDX39BATP6V1G2-DDX39B: 31,530,219–31,546,608, reverse strandATP6V1G2: 31,544,444–31,548,427, reverse strandNFKBIL1: 31,546,870–31,558,829, forward strandLTA: 31,572,054–31,574,324, forward strandLTATNF: 31,575,558–31,578,336, forward strandLTB: 31,580,525–31,582,522, reverse strandLST1: 31,581,065–31,588,911, forward strandLST1NCR3: 31,588,895–31,593,217, reverse strandNCR3AIF1: 31,615,214–31,617,025, forward strandAIF1PRRC2A: 31,620,675–31,637,771, forward strandPRRC2A: 31,622,774–31,622,860, forward strand: 31,623,874–31,625,499, forward strandBAG6: 31,638,543–31,652,747, reverse strandAPOM: 31,652,416–31,658,214, forward strandC6orf47: 31,658,298–31,660,778, reverse strandGPANK1: 31,661,228–31,666,283, reverse strandCSNK2B: 31,665,227–31,670,343, forward strand: 31,666,102–31,673,546, forward strandLY6G5B: 31,669,976–31,673,776, forward strandLY6G5C: 31,676,684–31,684,040, reverse strandLY6G5CABHD16A: 31,686,954–31,703,391, reverse strandABHD16ALY6G6F: 31,706,863–31,710,801, forward strandLY6G6F-LY6G6D: 31,706,904–31,717,918, forward strandLY6G6D: 31,715,285–31,717,919, forward strandMPIG6B: 31,718,594–31,726,714, forward strandLY6G6C: 31,718,648–31,721,746, reverse strandDDAH2: 31,726,586–31,730,617, reverse strandCLIC1: 31,730,579–31,740,558, reverse strandMSH5: 31,739,677–31,762,678, forward strandMSH5MSH5-SAPCD1: 31,740,020–31,764,851, forward strandSAPCD1: 31,762,656–31,764,851, forward strandVWA7: 31,765,590–31,777,328, reverse strandVWA7VARS1: 31,777,518–31,795,975, reverse strandLSM2: 31,797,019–31,806,992, reverse strandLSM2HSPA1L: 31,809,619–31,815,788, reverse strandHSPA1A: 31,815,543–31,817,994, forward strandHSPA1AHSPA1B: 31,827,738–31,830,254, forward strandHSPA1BNEU1: 31,857,063–31,862,905, reverse strandNEU1SLC44A4: 31,863,173–31,879,198, reverse strandSLC44A4EHMT2: 31,879,758–31,897,723, reverse strandEHMT2C2: 31,897,785–31,945,677, forward strandZBTB12: 31,899,065–31,902,103, reverse strandZBTB12: 31,927,698–31,952,048, forward strandCFB: 31,945,650–31,952,086, forward strandNELFE: 31,952,087–31,959,079, reverse strandNELFESKIC2: 31,959,175–31,969,751, forward strandSKIC2DXO: 31,969,810–31,972,517, reverse strandDXOWHR1: 31,971,091–31,982,821, forward strandWHR1C4A: 31,981,991–32,005,247, forward strandC4B: 32,014,725–32,035,975, forward strandC4BCYP21A2: 32,038,297–32,042,321, forward strandCYP21A2TNXB: 32,041,153–32,115,334, reverse strandTNXBATF6B: 32,115,264–32,128,255, reverse strandATF6BFKBPL: 32,128,697–32,131,070, reverse strandFKBPLPPT2: 32,146,580–32,163,679, forward strandPRRT1: 32,147,292–32,153,083, reverse strandPRRT1: 32,150,495–32,154,373, reverse strandPPT2-EGFL8: 32,153,845–32,171,978, forward strandEGFL8: 32,163,918–32,171,980, forward strandAGPAT1: 32,167,118–32,178,112, reverse strandRNF5: 32,178,391–32,184,769, forward strandAGER: 32,180,963–32,184,365, reverse strandPBX2: 32,184,733–32,190,278, reverse strandGPSM3: 32,190,766–32,195,523, reverse strandNOTCH4: 32,194,843–32,224,111, reverse strandNOTCH4TSBP1: 32,288,526–32,371,907, reverse strandTSBP1BTNL2: 32,391,481–32,407,181, reverse strandBTNL2HLA-DRA: 32,439,870–32,445,181, forward strandHLA-DRADiagram of SKIC2: 28 exons on the forward strand of chromosome 6Exon 3: 2 known disease-causing sitesExon 6: 1 known disease-causing siteExon 8: 3 known disease-causing sitesExon 9: 1 known disease-causing siteExon 10: 1 known disease-causing siteExon 11: 2 known disease-causing sitesExon 13: 1 known disease-causing siteExon 14: 1 known disease-causing siteExon 15: 2 known disease-causing sitesExon 16: 1 known disease-causing siteExon 17: 1 known disease-causing siteExon 20: 1 known disease-causing siteExon 22: 1 known disease-causing siteExon 24: 1 known disease-causing siteExon 25: 2 known disease-causing sitesExon 26: 2 known disease-causing sitesExon 28: 2 known disease-causing sitesExon 1: 31,959,175–31,959,214, 40 basesExon 2: 31,959,297–31,959,400, 104 basesExon 3: 31,960,010–31,960,119, 110 basesExon 4: 31,960,220–31,960,337, 118 basesExon 5: 31,960,432–31,960,546, 115 basesExon 6: 31,960,666–31,960,740, 75 basesExon 7: 31,961,041–31,961,094, 54 basesExon 8: 31,961,196–31,961,386, 191 basesExon 9: 31,961,547–31,961,675, 129 basesExon 10: 31,961,909–31,962,054, 146 basesExon 11: 31,962,439–31,962,585, 147 basesExon 12: 31,962,714–31,962,798, 85 basesExon 13: 31,962,985–31,963,091, 107 basesExon 14: 31,963,413–31,963,559, 147 basesExon 15: 31,963,637–31,963,733, 97 basesExon 16: 31,963,913–31,964,125, 213 basesExon 17: 31,964,232–31,964,342, 111 basesExon 18: 31,965,783–31,966,013, 231 basesExon 19: 31,966,709–31,966,846, 138 basesExon 20: 31,967,004–31,967,141, 138 basesExon 21: 31,967,273–31,967,377, 105 basesExon 22: 31,967,715–31,967,862, 148 basesExon 23: 31,967,956–31,968,082, 127 basesExon 24: 31,968,328–31,968,538, 211 basesExon 25: 31,968,686–31,968,796, 111 basesExon 26: 31,968,871–31,969,089, 219 basesExon 27: 31,969,280–31,969,420, 141 basesExon 28: 31,969,515–31,969,751, 237 bases1510152025285′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 3.8 kb of the gene's 10.6 kb; 3,741 of those bases code for the protein.

How a genome test reads SKIC2

32

positions in SKIC2 where ClinVar classes a change as pathogenic or likely pathogenic

32 of them (100%) fall in regions short reads find hard.

  • MHC (32 sites)The major histocompatibility complex (HLA genes), highly polymorphic and poorly represented by a single reference.

A whole genome covers all 10.6 kb of SKIC2, introns included, not only the 3.8 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.). SKIC2 gene: SKI2 subunit of superkiller complex. Retrieved 16 October 2026, from https://dantelabs.com/genes/skic2

Vancouver

Dante Labs. SKIC2 gene: SKI2 subunit of superkiller complex [Internet]. [cited 16 October 2026]. Available from: https://dantelabs.com/genes/skic2

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