AtlasGene
KCNQ1OT1
KCNQ1 opposite strand/antisense transcript 1
- HGNC 6295↗(opens in a new tab)
- Ensembl gene ENSG00000269821↗(opens in a new tab)
- NCBI Gene 10984↗(opens in a new tab)
Summary
- Cytogenetic location
- 11p15.5
- Coordinates
- Chromosome 11: 2,608,328–2,699,994 (GRCh38)
- Exons
- 1 exon across 91.7 kb
- Also known as
- KvDMR1, KCNQ1-AS2, KvLQT1-AS, LIT1, NCRNA00012
- MANE Select transcript
- ENST00000597346.1NR_002728.4
- Locus type
- Long non-coding RNA (lncRNA)
AtlasShare this page
This page as data
Add .json to the page's address, or ask for application/json, to read it as JSON.
library(jsonlite)
url <- "https://dantelabs.com/genes/kcnq1ot1.json"
page <- fromJSON(url)
page$gene$nameRead KCNQ1OT1, and the rest of your genome, with one test.
From $449Free shipping · Results in 6–8 weeks
Get my Genome TestCurated reports relevant to this gene
No Genome Test report reads KCNQ1OT1 yet. The test sequences your whole genome, so your data includes it all the same.
How KCNQ1OT1 is laid out
- Untranslated region
- Intron
- Direction of transcription
- Known disease-causing sites
- Stretches short reads find hard
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 91.7 kb of the gene's 91.7 kb.
Sequencing KCNQ1OT1
6Easy
How hard KCNQ1OT1 is to sequence with short reads, out of 100
0 · Easy100 · Hard
Almost all of KCNQ1OT1's exons sit where short reads map cleanly.
What adds to it: the share of KCNQ1OT1's exons in each kind of hard region
- MappabilityStretches where 100 or 250 bp reads cannot be placed uniquely, so a call there may be missing or wrong. On its own, a gene wholly in this kind of region would score 100.4.2%
- HomologySegmental duplications: copies elsewhere in the genome, such as paralogues and pseudogenes, at 90% identity or more. On its own, a gene wholly in this kind of region would score 60.0%
- Shared with chrYThe pseudoautosomal regions and the X-transposed region, where chrX and chrY carry the same or nearly the same sequence, so a read from one may be placed on the other. On its own, a gene wholly in this kind of region would score 60.0%
- Reference coverageGaps in the reference assembly nearby, where there is no sequence for reads to align to. On its own, a gene wholly in this kind of region would score 50.0%
- RepeatsTandem repeats and runs of one base, which reads slip on and may not span. On its own, a gene wholly in this kind of region would score 30.4.2%
- GC contentWindows under 25% or over 65% G and C, which library preparation covers thinly. On its own, a gene wholly in this kind of region would score 20.3%
A Dante Labs score from our own research, built on NIST's Genome in a Bottle maps of hard-to-sequence regions.How it's scoredEach bar is the share of KCNQ1OT1's exon bases in that kind of difficult region. Any one kind can make a gene hard on its own, and each further kind adds less: 0 when no base is in any, 100 when every base is where reads cannot be placed uniquely.
2
positions in KCNQ1OT1 where ClinVar classes a change as pathogenic or likely pathogenic
None of them falls in a region short reads find hard.
A whole genome covers all 91.7 kb of KCNQ1OT1, introns included, not only the 91.7 kb of exons.
ClinVar pathogenic variants (2)
The KCNQ1OT1 variants ClinVar classifies pathogenic or likely pathogenic for any condition, reviewed by at least one submitter with criteria, and the most reviewed of them. It is ClinVar's public record of the gene, never a result.
- Likely pathogenic 2
| Variant | Conditions | ClinVar classification | Review status |
|---|---|---|---|
| NM_000218.3(KCNQ1):c.1451_1452del (p.Ser484fs) (opens in a new tab) | long QT syndrome 1 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
| NM_000218.3(KCNQ1):c.1454_1458del (p.Ser484_Phe485insTer) (opens in a new tab) | long QT syndrome 1 | Likely pathogenic | ★★★★1 star out of 4 criteria provided, single submitter |
Traits linked to KCNQ1OT1
The Human Phenotype Ontology lists these as features of the rare conditions KCNQ1OT1 can cause. Each trait's page lists the other genes linked to it.
Abnormality of head or neck
- Abnormal dentition
- Facial asymmetry
- Dandy-Walker malformation
- Abnormally large tongue
- Coarse facial features
- Midface retrusion
- Prominent back of the head
- Prominent metopic ridge
Show 1 more trait
Abnormality of the genitourinary system
- Nephroblastoma
- Undescended testes
- Enlarged kidney
- Gonadoblastoma
- Increased calcium level in kidney
- Kidney stone
- Overgrowth of external genitalia
- Renal cortical cysts
Show 1 more trait
External links
Gene records
Transcript
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.
- ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
- The Genome in a Bottle genome stratifications, from NIST: the sequencing difficulty score.
- The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
- Data release 2026.10.19-9814e911.
Cite this page
Dante Labs. (n.d.). KCNQ1OT1 gene: KCNQ1 opposite strand/antisense transcript 1. Retrieved 21 October 2026, from https://dantelabs.com/genes/kcnq1ot1
Dante Labs. KCNQ1OT1 gene: KCNQ1 opposite strand/antisense transcript 1 [Internet]. [cited 21 October 2026]. Available from: https://dantelabs.com/genes/kcnq1ot1
AtlasOne test. A lifetime of answers.
From $449Free shipping · Results in 6–8 weeks