KCNQ1OT1

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

Basic information

Region (hg38): 11:2597308-2700003

Links

ENSG00000269821 ∙ NCBI:10984 ∙ OMIM:604115 ∙ HGNC:6295 ∙ ∙ ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Beckwith-Wiedemann syndrome (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Beckwith-Wiedemann syndrome	AD	Endocrine; Oncologic	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	Craniofacial; Endocrine; Gastrointestinal; Genitourinary; Musculoskeletal; Neurologic; Oncologic; Renal	11181570; 12019213; 12772698; 20301568; 20803657; 21920939
The condition can involve imprinting defects affecting the gene (an antisense transcript for KCNQ1).

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KCNQ1OT1 gene.

• not provided (393 variants)
• Long QT syndrome (56 variants)
• Cardiac arrhythmia (38 variants)
• Cardiovascular phenotype (18 variants)
• not specified (13 variants)
• Congenital long QT syndrome (13 variants)
• Long QT syndrome 1 (11 variants)
• Short QT syndrome (7 variants)
• Jervell and Lange-Nielsen syndrome 1 (7 variants)
• Familial atrial fibrillation (7 variants)
• Jervell and Lange-Nielsen syndrome (7 variants)
• Atrial fibrillation, familial, 3 (6 variants)
• Short QT syndrome type 2 (6 variants)
• Inborn genetic diseases (2 variants)
• KCNQ1-related epilepsy (1 variants)
• Autosomal dominant KCNQ1-related disease (1 variants)
• Prolonged QT interval (1 variants)
• Short QT syndrome type 2;Long QT syndrome 1;Jervell and Lange-Nielsen syndrome 1;Atrial fibrillation, familial, 3;Beckwith-Wiedemann syndrome (1 variants)
• Sudden cardiac death (1 variants)
• Long QT syndrome 1;Jervell and Lange-Nielsen syndrome 1;Atrial fibrillation, familial, 3;Beckwith-Wiedemann syndrome;Short QT syndrome type 2 (1 variants)
• Jervell and Lange-Nielsen syndrome 1;Long QT syndrome 1;Short QT syndrome type 2;Atrial fibrillation, familial, 3;Beckwith-Wiedemann syndrome (1 variants)
• Silver-Russell syndrome 1 (1 variants)
• Atrial fibrillation, familial, 3;Beckwith-Wiedemann syndrome;Short QT syndrome type 2;Long QT syndrome 1;Jervell and Lange-Nielsen syndrome 1 (1 variants)
• KCNQ1OT1-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KCNQ1OT1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	8	5	59	145	240	457
Total	8	5	59	145	240

Variants in KCNQ1OT1

This is a list of pathogenic ClinVar variants found in the KCNQ1OT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
11-2608632-C-CA		KCNQ1-related disorder	Benign (Oct 01, 2022)
11-2609472-A-C		KCNQ1-related disorder	Benign (Nov 01, 2024)
11-2609499-G-C			Benign (Nov 01, 2024)
11-2609583-CTTCT-C			Benign (Oct 01, 2022)
11-2610111-T-C			Likely benign (Nov 01, 2024)
11-2610334-C-T			Benign (Sep 01, 2024)
11-2610380-C-T		Short QT syndrome • Familial atrial fibrillation • Jervell and Lange-Nielsen syndrome • Long QT syndrome • Congenital long QT syndrome	Likely benign (Jun 14, 2016)
11-2610392-C-T		Congenital long QT syndrome • Long QT syndrome • Jervell and Lange-Nielsen syndrome • Familial atrial fibrillation • Short QT syndrome	Likely benign (Jun 14, 2016)
11-2610436-A-G		KCNQ1-related disorder	Likely benign (Sep 03, 2021)
11-2610563-T-C		KCNQ1-related disorder	Likely benign (Jul 27, 2023)
11-2610716-CTTTTTTTTT-C			Benign (Aug 01, 2022)
11-2610716-CTTTTTTTTTTT-C			Benign (Sep 01, 2023)
11-2610772-C-G			Uncertain significance (Jun 01, 2024)
11-2611003-A-T		KCNQ1-related disorder	Likely benign (Aug 01, 2024)
11-2611248-C-T			Benign (Apr 01, 2024)
11-2611281-G-A			Benign (Jan 01, 2023)
11-2611322-C-A			Likely benign (Nov 01, 2023)
11-2611500-C-G		Short QT syndrome • Jervell and Lange-Nielsen syndrome • Familial atrial fibrillation • Congenital long QT syndrome • Long QT syndrome	Likely benign (Jun 14, 2016)
11-2611913-GC-G			Likely benign (Nov 01, 2024)
11-2612206-T-C			Likely benign (Mar 01, 2024)
11-2612222-TC-T		KCNQ1-related disorder	Likely benign (Apr 05, 2023)
11-2612485-G-C		KCNQ1-related disorder	Benign (Oct 28, 2019)
11-2612496-ATTCT-A			Likely benign (May 01, 2023)
11-2612499-C-G			Likely benign (May 01, 2024)
11-2612582-T-C			Benign (Jul 01, 2024)

GnomAD

Source: gnomAD

dbNSFP

Source: dbNSFP

Essentials

• gene_indispensability_pred: N
• gene_indispensability_score: 0.283

Mouse Genome Informatics

• Gene name: Kcnq1ot1
• Phenotype: growth/size/body region phenotype; cellular phenotype; normal phenotype; embryo phenotype; liver/biliary system phenotype; respiratory system phenotype; renal/urinary system phenotype