chr11:2588804:C>G Detail (hg38) (KCNQ1)

Information

Genome

Assembly Position
hg19 chr11:2,610,034-2,610,034 View the variant detail on this assembly version.
hg38 chr11:2,588,804-2,588,804

HGVS

Type Transcript Protein
RefSeq NM_000218.2:c.1343C>G NP_000209.2:p.Pro448Arg
NM_181798.1:c.962C>G NP_861463.1:p.Pro321Arg
Ensemble ENST00000155840.12:c.1343C>G ENST00000155840.12:p.Pro448Arg
Summary

MGeND

Clinical significance Pathogenic
Variant entry 3
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.101
ToMMo:0.101
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.098

Prediction

ClinVar

Clinical Significance Benign Likely benign
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 tgv41369710 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
(TMGS000137) 		Kenjiro Kosaki Keio University
Pathogenic jervell and lange-nielsen syndrome germline MGS000001
(TMGS000137) 		Kenjiro Kosaki Keio University
Pathogenic long qt syndrome germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2020-03-11 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2018-06-20 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign Likely benign 2024-02-01 criteria provided, multiple submitters, no conflicts long QT syndrome germline unknown Detail
Benign 2015-04-21 criteria provided, single submitter germline Detail
Benign 2018-03-06 criteria provided, single submitter long QT syndrome 1 germline Detail
Benign 2018-03-06 criteria provided, single submitter Atrial fibrillation, familial, 3 germline Detail
Benign 2018-03-06 criteria provided, single submitter Jervell and Lange-Nielsen syndrome 1 germline Detail
Benign 2018-03-06 criteria provided, single submitter Short QT syndrome type 2 germline Detail
Benign 2018-03-19 criteria provided, single submitter Cardiac arrhythmia germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.132 Congenital long QT syndrome Given the inconsistencies between the genotype (LQT1) and clinical phenotype (LQ... BeFree 15242738 Detail
0.133 Congenital long QT syndrome Given the inconsistencies between the genotype (LQT1) and clinical phenotype (LQ... BeFree 15242738 Detail
0.133 Congenital long QT syndrome NA CLINVAR Detail
0.573 Romano-Ward Syndrome NA CLINVAR Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000218.3(KCNQ1):c.1343C>G (p.Pro448Arg) AND not provided ClinVar Detail
NM_000218.3(KCNQ1):c.1343C>G (p.Pro448Arg) AND not specified ClinVar Detail
NM_000218.3(KCNQ1):c.1343C>G (p.Pro448Arg) AND Long QT syndrome ClinVar Detail
NM_000218.3(KCNQ1):c.1343C>G (p.Pro448Arg) AND Cardiovascular phenotype ClinVar Detail
NM_000218.3(KCNQ1):c.1343C>G (p.Pro448Arg) AND Long QT syndrome 1 ClinVar Detail
NM_000218.3(KCNQ1):c.1343C>G (p.Pro448Arg) AND Atrial fibrillation, familial, 3 ClinVar Detail
NM_000218.3(KCNQ1):c.1343C>G (p.Pro448Arg) AND Jervell and Lange-Nielsen syndrome 1 ClinVar Detail
NM_000218.3(KCNQ1):c.1343C>G (p.Pro448Arg) AND Short QT syndrome type 2 ClinVar Detail
NM_000218.3(KCNQ1):c.1343C>G (p.Pro448Arg) AND Cardiac arrhythmia ClinVar Detail
Given the inconsistencies between the genotype (LQT1) and clinical phenotype (LQT2) in our two LQTS ... DisGeNET Detail
Given the inconsistencies between the genotype (LQT1) and clinical phenotype (LQT2) in our two LQTS ... DisGeNET Detail
NA 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
rs12720449 dbSNP
Genome
hg38
Position
chr11:2,588,804-2,588,804
Variant Type
snv
Reference Allele
C
Alternative Allele
G
Filtering Status (HGVD)
PASS
# of samples (HGVD)
862
Mean of sample read depth (HGVD)
15.07
Standard deviation of sample read depth (HGVD)
8.07
Number of reference allele (HGVD)
1550
Number of alternative allele (HGVD)
174
Allele Frequency (HGVD)
0.10092807424593968
Gene Symbol (HGVD)
KCNQ1
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))
rs12720449
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1009
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
1691
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8546
East Asian Allele Counts (ExAC)
841
East Asian Heterozygous Counts (ExAC)
767
East Asian Homozygous Counts (ExAC)
37
East Asian Allele Frequency (ExAC)
0.09840861221624152
Chromosome Counts in All Race (ExAC)
118590
Allele Counts in All Race (ExAC)
903
Heterozygous Counts in All Race (ExAC)
828
Homozygous Counts in All Race (ExAC)
37
Allele Frequency in All Race (ExAC)
0.007614470022767519
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