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KCNQ1OT1 gene

KCNQ1 opposite strand/antisense transcript 1

Normal Function

The KCNQ1OT1 gene is located within another gene, KCNQ1. Because the two genes share a region of overlapping DNA, the KCNQ1OT1 gene is also known as KCNQ1 overlapping transcript 1 or KCNQ1 opposite strand/antisense transcript 1. The DNA sequence of two genes is "read" in opposite directions, and the genes have very different functions. Unlike the KCNQ1 gene, which provides instructions for making a protein that acts as a potassium channel, the KCNQ1OT1 gene does not contain instructions for making a protein. Instead, a molecule called a noncoding RNA (a chemical cousin of DNA) is produced from the KCNQ1OT1 gene. This RNA helps regulate genes that are essential for normal growth and development before birth.

People inherit one copy of most genes from their mother and one copy from their father. Both copies are typically active, or "turned on," in cells. However, the activity of the KCNQ1OT1 gene depends on which parent it was inherited from. Only the copy inherited from a person's father (the paternally inherited copy) is active; the copy inherited from the mother (the maternally inherited copy) is not active. This sort of parent-specific difference in gene activation is caused by a phenomenon called genomic imprinting.

The KCNQ1OT1 gene is part of a cluster of genes on the short (p) arm of chromosome 11 that undergo genomic imprinting. KCNQ1OT1 and several other genes in this cluster that are thought to help regulate growth are controlled by a nearby region of DNA known as imprinting center 2 (IC2) or KvDMR. The IC2 region undergoes a process called methylation, which is a chemical reaction that attaches small molecules called methyl groups to certain segments of DNA. Methylation, which occurs during the formation of an egg or sperm cell, is a way of marking or "stamping" the parent of origin. The IC2 region is normally methylated only on the maternally inherited copy of chromosome 11.

Health Conditions Related to Genetic Changes

Beckwith-Wiedemann syndrome

Beckwith-Wiedemann syndrome is a condition characterized by overgrowth and other signs and symptoms that affect many parts of the body. At least half of all cases of this condition result from changes in a process called methylation that affects the IC2 region. Specifically, the maternally inherited copy of the IC2 region has too few methyl groups attached (hypomethylation). This abnormality disrupts the regulation of several genes that are normally controlled by IC2. Hypomethylation of the IC2 region leads to an increase in the activity of the KCNQ1OT1 gene and a reduction in the activity of other nearby genes. Because some of these genes are involved in directing growth, a loss of their activity leads to overgrowth and the other features of Beckwith-Wiedemann syndrome.

In a few cases, Beckwith-Wiedemann syndrome has been caused by deletions of a small amount of DNA from the maternally inherited copy of the IC2 region. Like abnormal methylation, these deletions disrupt the activity of several genes, including KCNQ1OT1.

More About This Health Condition

Other Names for This Gene

  • FLJ41078
  • KCNQ1 opposite strand/antisense transcript 1 (non-protein coding)
  • KCNQ1 overlapping transcript 1
  • KCNQ1 overlapping transcript 1 (non-protein coding)
  • KCNQ1-AS2
  • KCNQ10T1
  • KvDMR1
  • KvLQT1-AS
  • LIT1
  • long QT intronic transcript 1

Additional Information & Resources

Tests Listed in the Genetic Testing Registry

Scientific Articles on PubMed

Catalog of Genes and Diseases from OMIM

Gene and Variant Databases


  • Bliek J, Maas SM, Ruijter JM, Hennekam RC, Alders M, Westerveld A, Mannens MM. Increased tumour risk for BWS patients correlates with aberrant H19 and not KCNQ1OT1 methylation: occurrence of KCNQ1OT1 hypomethylation in familial cases of BWS. Hum Mol Genet. 2001 Mar 1;10(5):467-76. doi: 10.1093/hmg/10.5.467. Citation on PubMed
  • Chiesa N, De Crescenzo A, Mishra K, Perone L, Carella M, Palumbo O, Mussa A, Sparago A, Cerrato F, Russo S, Lapi E, Cubellis MV, Kanduri C, Cirillo Silengo M, Riccio A, Ferrero GB. The KCNQ1OT1 imprinting control region and non-coding RNA: new properties derived from the study of Beckwith-Wiedemann syndrome and Silver-Russell syndrome cases. Hum Mol Genet. 2012 Jan 1;21(1):10-25. doi: 10.1093/hmg/ddr419. Epub 2011 Sep 14. Citation on PubMed or Free article on PubMed Central
  • Du M, Zhou W, Beatty LG, Weksberg R, Sadowski PD. The KCNQ1OT1 promoter, a key regulator of genomic imprinting in human chromosome 11p15.5. Genomics. 2004 Aug;84(2):288-300. doi: 10.1016/j.ygeno.2004.03.008. Citation on PubMed
  • Kanduri C. Functional insights into long antisense noncoding RNA Kcnq1ot1 mediated bidirectional silencing. RNA Biol. 2008 Oct-Dec;5(4):208-11. doi: 10.4161/rna.7113. Epub 2008 Oct 3. Citation on PubMed
  • Kanduri C. Kcnq1ot1: a chromatin regulatory RNA. Semin Cell Dev Biol. 2011 Jun;22(4):343-50. doi: 10.1016/j.semcdb.2011.02.020. Epub 2011 Feb 21. Citation on PubMed
  • Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Nagano T, Mancini-Dinardo D, Kanduri C. Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell. 2008 Oct 24;32(2):232-46. doi: 10.1016/j.molcel.2008.08.022. Citation on PubMed
  • Thakur N, Tiwari VK, Thomassin H, Pandey RR, Kanduri M, Gondor A, Grange T, Ohlsson R, Kanduri C. An antisense RNA regulates the bidirectional silencing property of the Kcnq1 imprinting control region. Mol Cell Biol. 2004 Sep;24(18):7855-62. doi: 10.1128/MCB.24.18.7855-7862.2004. Citation on PubMed or Free article on PubMed Central
  • Weksberg R, Nishikawa J, Caluseriu O, Fei YL, Shuman C, Wei C, Steele L, Cameron J, Smith A, Ambus I, Li M, Ray PN, Sadowski P, Squire J. Tumor development in the Beckwith-Wiedemann syndrome is associated with a variety of constitutional molecular 11p15 alterations including imprinting defects of KCNQ1OT1. Hum Mol Genet. 2001 Dec 15;10(26):2989-3000. doi: 10.1093/hmg/10.26.2989. Citation on PubMed

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