chr11:2790111:C>T Detail (hg19) (KCNQ1)

Information

Genome

Assembly Position
hg19 chr11:2,790,111-2,790,111
hg38 chr11:2,768,881-2,768,881 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_181798.1:c.1171C>T NP_861463.1:p.Arg391Ter
NM_000218.2:c.1552C>T NP_000209.2:p.Arg518Ter
Ensemble ENST00000335475.6:c.1171C>T ENST00000335475.6:p.Arg391Ter
Summary

MGeND

Clinical significance Pathogenic
Variant entry 2
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:[No Data.]
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:<0.001

Prediction

ClinVar

Clinical Significance Pathogenic
Review star
Show details
Links
Type Database ID Link
Gene MIM 607542 OMIM
HGNC 6294 HGNC
Ensembl ENSG00000053918 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv41374096 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic long qt syndrome germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
Pathogenic long qt syndrome germline MGS000001
(TMGS000174) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Pathogenic 2003-05-08 no assertion criteria provided Long QT syndrome 1, recessive germline Detail
Pathogenic 2024-02-05 criteria provided, multiple submitters, no conflicts long QT syndrome germline Detail
Pathogenic 2021-04-23 criteria provided, multiple submitters, no conflicts not provided germline Detail
Pathogenic 2021-09-15 criteria provided, single submitter germline Detail
Pathogenic 2023-05-03 criteria provided, multiple submitters, no conflicts long QT syndrome 1 de novo germline unknown Detail
Pathogenic 2019-10-02 criteria provided, single submitter Congenital long QT syndrome germline Detail
Pathogenic 2018-10-23 criteria provided, multiple submitters, no conflicts KCNQ1-related disorder germline Detail
Pathogenic 2018-07-12 criteria provided, single submitter not specified germline Detail
Pathogenic 2019-06-10 criteria provided, single submitter Conduction disorder of the heart germline Detail
Pathogenic 2023-12-18 criteria provided, single submitter Cardiac arrhythmia germline Detail
not provided no assertion provided Jervell and Lange-Nielsen syndrome 1 germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.417 long QT syndrome NA CLINVAR Detail
0.002 Congenital deafness These data extend the range of known KCNQ1 mutations associated with both recess... BeFree 10737999 Detail
0.573 Romano-Ward Syndrome The nonsense mutations R518X-KCNQ1 and Q530X-KCNQ1 cause LQT1 (long-QT syndrome ... BeFree 22309168 Detail
0.417 long QT syndrome Phenotype, origin and estimated prevalence of a common long QT syndrome mutation... BeFree 24552659 Detail
<0.001 Gastric Carcinoid Tumor An adult female with Jervell and Lange-Nielsen syndrome (JLNS; with KCNQ1 nonsen... BeFree 21118729 Detail
0.133 Congenital long QT syndrome These data extend the range of known KCNQ1 mutations associated with both recess... BeFree 10737999 Detail
0.585 Jervell-Lange Nielsen syndrome The R518X/KCNQ1 mutation is a common cause of autosomal recessive (Jervell and L... BeFree 24552659 Detail
<0.001 Gastric Carcinoid Tumor An adult female with Jervell and Lange-Nielsen syndrome (JLNS; with KCNQ1 nonsen... BeFree 21118729 Detail
0.133 Congenital long QT syndrome NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000218.3(KCNQ1):c.1552C>T (p.Arg518Ter) AND Long QT syndrome 1, recessive ClinVar Detail
NM_000218.3(KCNQ1):c.1552C>T (p.Arg518Ter) AND Long QT syndrome ClinVar Detail
NM_000218.3(KCNQ1):c.1552C>T (p.Arg518Ter) AND not provided ClinVar Detail
NM_000218.3(KCNQ1):c.1552C>T (p.Arg518Ter) AND Cardiovascular phenotype ClinVar Detail
NM_000218.3(KCNQ1):c.1552C>T (p.Arg518Ter) AND Long QT syndrome 1 ClinVar Detail
NM_000218.3(KCNQ1):c.1552C>T (p.Arg518Ter) AND Congenital long QT syndrome ClinVar Detail
NM_000218.3(KCNQ1):c.1552C>T (p.Arg518Ter) AND KCNQ1-related disorder ClinVar Detail
NM_000218.3(KCNQ1):c.1552C>T (p.Arg518Ter) AND not specified ClinVar Detail
NM_000218.3(KCNQ1):c.1552C>T (p.Arg518Ter) AND Conduction disorder of the heart ClinVar Detail
NM_000218.3(KCNQ1):c.1552C>T (p.Arg518Ter) AND Cardiac arrhythmia ClinVar Detail
NM_000218.3(KCNQ1):c.1552C>T (p.Arg518Ter) AND Jervell and Lange-Nielsen syndrome 1 ClinVar Detail
NA DisGeNET Detail
These data extend the range of known KCNQ1 mutations associated with both recessive and dominant for... DisGeNET Detail
The nonsense mutations R518X-KCNQ1 and Q530X-KCNQ1 cause LQT1 (long-QT syndrome type 1) and result i... DisGeNET Detail
Phenotype, origin and estimated prevalence of a common long QT syndrome mutation: a clinical, geneal... DisGeNET Detail
An adult female with Jervell and Lange-Nielsen syndrome (JLNS; with KCNQ1 nonsense mutations p.Arg51... DisGeNET Detail
These data extend the range of known KCNQ1 mutations associated with both recessive and dominant for... DisGeNET Detail
The R518X/KCNQ1 mutation is a common cause of autosomal recessive (Jervell and Lange Nielsen Syndrom... DisGeNET Detail
An adult female with Jervell and Lange-Nielsen syndrome (JLNS; with KCNQ1 nonsense mutations p.Arg51... DisGeNET Detail
NA DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs17215500 dbSNP
Genome
hg19
Position
chr11:2,790,111-2,790,111
Variant Type
snv
Reference Allele
C
Alternative Allele
T
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs17215500
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8650
East Asian Allele Counts (ExAC)
0
East Asian Heterozygous Counts (ExAC)
0
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.0
Chromosome Counts in All Race (ExAC)
121128
Allele Counts in All Race (ExAC)
20
Heterozygous Counts in All Race (ExAC)
20
Homozygous Counts in All Race (ExAC)
0
Allele Frequency in All Race (ExAC)
1.6511458952513043E-4
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