Skip Navigation
Genetics Home Reference: your guide to understanding genetic conditions     A service of the U.S. National Library of Medicine®


Reviewed April 2008

What is the official name of the KCNQ1OT1 gene?

The official name of this gene is “KCNQ1 opposite strand/antisense transcript 1 (non-protein coding).”

KCNQ1OT1 is the gene's official symbol. The KCNQ1OT1 gene is also known by other names, listed below.

What is the normal function of the KCNQ1OT1 gene?

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, however, 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. The KCNQ1OT1 gene, however, is active only when it is inherited from a person's father. 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 are controlled by a nearby region of DNA known as imprinting center 2 (ICR2) or KvDMR. The KCNQ1OT1 gene plays an important role in maintaining the genomic imprinting of these genes. Several of the genes in this cluster are thought to help regulate growth.

How are changes in the KCNQ1OT1 gene related to health conditions?

Beckwith-Wiedemann syndrome - associated with the KCNQ1OT1 gene

At least half of all cases of Beckwith-Wiedemann result from changes in a process called methylation that affects the ICR2 region. In genes that undergo genomic imprinting, the parent of origin is often marked, or "stamped," on the gene during the formation of egg and sperm cells. This stamping process, called methylation, is a chemical reaction that attaches small molecules called methyl groups to certain segments of DNA.

In many people with Beckwith-Wiedemann syndrome, the ICR2 region has too few methyl groups attached (hypomethylation). This abnormality disrupts the regulation of several genes that are normally controlled by ICR2. Specifically, hypomethylation of the ICR2 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, an increased risk of tumors, 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 ICR2 region. Like abnormal methylation, these deletions disrupt the activity of several genes, including KCNQ1OT1.

Where is the KCNQ1OT1 gene located?

Cytogenetic Location: 11p15

Molecular Location on chromosome 11: base pairs 2,608,327 to 2,699,997

The KCNQ1OT1 gene is located on the short (p) arm of chromosome 11 at position 15.

The KCNQ1OT1 gene is located on the short (p) arm of chromosome 11 at position 15.

More precisely, the KCNQ1OT1 gene is located from base pair 2,608,327 to base pair 2,699,997 on chromosome 11.

See How do geneticists indicate the location of a gene? ( in the Handbook.

Where can I find additional information about KCNQ1OT1?

You and your healthcare professional may find the following resources about KCNQ1OT1 helpful.

You may also be interested in these resources, which are designed for genetics professionals and researchers.

What other names do people use for the KCNQ1OT1 gene or gene products?

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

See How are genetic conditions and genes named? ( in the Handbook.

What glossary definitions help with understanding KCNQ1OT1?

channel ; chromosome ; DNA ; egg ; epigenetic ; gene ; imprinting ; inherit ; inherited ; methyl ; methylation ; molecule ; potassium ; protein ; RNA ; sperm ; syndrome ; transcript

You may find definitions for these and many other terms in the Genetics Home Reference Glossary (


  • 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. (
  • Delaval K, Wagschal A, Feil R. Epigenetic deregulation of imprinting in congenital diseases of aberrant growth. Bioessays. 2006 May;28(5):453-9. Review. (
  • Diaz-Meyer N, Yang Y, Sait SN, Maher ER, Higgins MJ. Alternative mechanisms associated with silencing of CDKN1C in Beckwith-Wiedemann syndrome. J Med Genet. 2005 Aug;42(8):648-55. (
  • 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. (
  • Enklaar T, Zabel BU, Prawitt D. Beckwith-Wiedemann syndrome: multiple molecular mechanisms. Expert Rev Mol Med. 2006 Jul 17;8(17):1-19. Review. (
  • NCBI Gene (
  • Niemitz EL, DeBaun MR, Fallon J, Murakami K, Kugoh H, Oshimura M, Feinberg AP. Microdeletion of LIT1 in familial Beckwith-Wiedemann syndrome. Am J Hum Genet. 2004 Nov;75(5):844-9. Epub 2004 Sep 15. (
  • Thakur N, Tiwari VK, Thomassin H, Pandey RR, Kanduri M, Göndör 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. (
  • 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. (
  • Weksberg R, Shuman C, Smith AC. Beckwith-Wiedemann syndrome. Am J Med Genet C Semin Med Genet. 2005 Aug 15;137C(1):12-23. Review. (


The resources on this site should not be used as a substitute for professional medical care or advice. Users seeking information about a personal genetic disease, syndrome, or condition should consult with a qualified healthcare professional. See How can I find a genetics professional in my area? ( in the Handbook.

Reviewed: April 2008
Published: February 23, 2015