KCNQ1OT1

ncRNA

KCNQ1 opposite strand/antisense transcript 1, the group of Long non-coding RNAs with non-systematic symbols

Gene summary

Human chromosomal region 11p15.5 contains two clusters of epigenetically-regulated genes that are expressed from only one chromosome in a parent-of-origin manner. Each cluster, or imprinted domain, is regulated by a functionally independent imprinting control region (ICR). The human CDKN1C/KCNQ1OT1 domain is regulated by an ICR located in an intron of KCNQ1, and contains at least eight genes that are expressed exclusively or preferentially from the maternally-inherited allele. The DNA of the ICR is specifically methylated on the maternally-inherited chromosome, and unmethylated on the paternally-inherited chromosome. The ICR contains the promoter of the KCNQ1OT1 gene that is exclusively expressed from the paternal allele. The KCNQ1OT1 transcript is the antisense to the KCNQ1 gene and is a unspliced long non-coding RNA. It interacts with chromatin and regulates transcription of multiple target genes through epigenetic modifications. The transcript is abnormally expressed from both chromosomes in most patients with Beckwith-Wiedemann syndrome, and the transcript also plays an important role in colorectal carcinogenesis. [provided by RefSeq, Apr 2012]

MANE transcript

N/A

Inheritance

ClinVar variants

—

Top phenotype

Beckwith-Wiedemann syndrome

Max pathogenic AF

—

Genomic locus

chr11:2,597,308-2,700,003

External References & Databases

Ensembl (ENSG00000269821)

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Beckwith-Wiedemann syndromeLIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0007534

Submitter: Labcorp Genetics (formerly Invitae)

Beckwith-Wiedemann syndromeLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0007534

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Beckwith-Wiedemann syndromeAD

Manifestation: Craniofacial; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Oncologic; Renal

Intervention: Endocrine; Oncologic

Rationale: In Beckwith-Wiedemann syndrome, surveillance and early detection of and treatment for malignancy may decrease morbidity and mortality; Recognition and surveillance for and treatment of neonatal hypoglycemia can be beneficial

Comments: The condition can involve imprinting defects affecting the gene (an antisense transcript for KCNQ1).

Refs: 11181570; 12019213; 12772698; 20301568; 20803657; 21920939

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KCNQ1OT1 variants in ClinVar

24 Conditions Cataloged

not providedTotal: 393

Long QT syndromeTotal: 56

Cardiac arrhythmiaTotal: 38

Cardiovascular phenotypeTotal: 18

not specifiedTotal: 13

Congenital long QT syndromeTotal: 13

Long QT syndrome 1Total: 11

Short QT syndromeTotal: 7

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB
synonymous
missense
nonsense
start loss
frameshift
splice donor/acceptor (+/-2bp)
Total	0	0	0	0	0

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 0 of 0 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
No transcripts match your selected source or search query.

dbNSFP Gene Annotations

Source: dbNSFP

Essentials

Indispensability pred.: N
Indispensability score: 0.283