chr21:34449382:C>T Detail (hg38) (KCNE1)

Information

Genome

Assembly Position
hg19 chr21:35,821,680-35,821,680 View the variant detail on this assembly version.
hg38 chr21:34,449,382-34,449,382

HGVS

Type Transcript Protein
RefSeq NM_001270402.2:c.253G>A NP_001257331.1:p.Asp85Asn
NM_001270403.2:c.253G>A NP_001257332.1:p.Asp85Asn
NM_000219.5:c.253G>A NP_000210.2:p.Asp85Asn
Summary

MGeND

Clinical significance Benign Likely pathogenic Pathogenic
Variant entry 4
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.015
ToMMo:0.011
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.006

Prediction

ClinVar

Clinical Significance Conflicting classifications of pathogenicity; other; risk factor
Review star
Show details
Links
Type Database ID Link
Gene MIM 176261 OMIM
HGNC 6240 HGNC
Ensembl ENSG00000180509 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv64916829 TogoVar
COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Pathogenic other germline MGS000001
(TMGS000137) 		Kenjiro Kosaki Keio University
Likely pathogenic long qt syndrome germline MGS000001
(TMGS000137) 		Kenjiro Kosaki Keio University
Benign Centenarian germline MGS000068
(TMGS000140) 		Kenjiro Kosaki Keio University
Pathogenic other germline MGS000001
(TMGS000154) 		Kenjiro Kosaki Keio University
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
risk factor 2006-08-01 no assertion criteria provided Long QT syndrome 5, acquired, susceptibility to germline Detail
no classifications from unflagged records 2024-02-09 no classifications from unflagged records Long QT syndrome 2/5, digenic germline Detail
Benign Likely benign 2023-09-25 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign; other 2024-03-01 criteria provided, multiple submitters, no conflicts not provided germline unknown Detail
Benign Likely benign 2022-11-01 criteria provided, multiple submitters, no conflicts long QT syndrome germline unknown Detail
Likely benign 2018-06-25 criteria provided, single submitter germline Detail
Conflicting interpretations of pathogenicity 2018-10-15 criteria provided, conflicting interpretations Jervell and Lange-Nielsen syndrome 2 germline unknown Detail
Likely benign; risk factor 2017-06-08 criteria provided, multiple submitters, no conflicts long QT syndrome 5 germline Detail
Benign 2019-04-01 criteria provided, single submitter cardiomyopathy germline Detail
Likely benign; risk factor 2020-03-04 criteria provided, multiple submitters, no conflicts Congenital long QT syndrome germline Detail
Uncertain significance 2021-03-30 criteria provided, single submitter long QT syndrome 5,Jervell and Lange-Nielsen syndrome 2 germline Detail
Uncertain significance 2021-03-30 criteria provided, single submitter long QT syndrome 5,Jervell and Lange-Nielsen syndrome 2 germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.280 long QT syndrome NA CLINVAR Detail
0.122 Congenital long QT syndrome Screening the family members for three LQTS modifiers (rs4657139 and rs16847548 ... BeFree 22708720 Detail
<0.001 Congenital long QT syndrome Screening the family members for three LQTS modifiers (rs4657139 and rs16847548 ... BeFree 22708720 Detail
0.122 Congenital long QT syndrome Genetic screening identified a KCNE1 D85N variant, which has been reported to be... BeFree 20823649 Detail
<0.001 Tachycardia During the tachycardia phase following adenosine, QTc increased to 620 ms. Genet... BeFree 21712262 Detail
0.280 long QT syndrome Instability of KCNE1-D85N that causes long QT syndrome: stabilization by verapam... BeFree 24499369 Detail
0.120 Long QT syndrome 5, acquired, susceptibility to NA CLINVAR Detail
0.280 long QT syndrome D85N, a KCNE1 polymorphism, is a disease-causing gene variant in long QT syndrom... BeFree 19695459 Detail
0.003 Torsades de pointes Drug-induced QT-interval prolongation and recurrent torsade de pointes in a chil... BeFree 22999324 Detail
0.417 long QT syndrome The common KCNE1 D85N potassium channel variant prolongs QT interval by inhibiti... BeFree 21244686 Detail
0.280 long QT syndrome Screening of the genotype disclosed the KCNE1 D85N polymorphism, which is known ... BeFree 22999324 Detail
0.388 long QT syndrome The common KCNE1 D85N potassium channel variant prolongs QT interval by inhibiti... BeFree 21244686 Detail
<0.001 cardiac arrest Aborted cardiac arrest in a patient carrying KCNE1 D85N variant during the postp... BeFree 20823649 Detail
0.003 Torsades de pointes A large candidate gene survey identifies the KCNE1 D85N polymorphism as a possib... BeFree 22100668 Detail
0.280 long QT syndrome KCNE1 D85N polymorphism--a sex-specific modifier in type 1 long QT syndrome? BeFree 21244686 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_000219.6(KCNE1):c.253G>A (p.Asp85Asn) AND Long QT syndrome 5, acquired, susceptibility to ClinVar Detail
NM_000219.6(KCNE1):c.253G>A (p.Asp85Asn) AND Long QT syndrome 2/5, digenic ClinVar Detail
NM_000219.6(KCNE1):c.253G>A (p.Asp85Asn) AND not specified ClinVar Detail
NM_000219.6(KCNE1):c.253G>A (p.Asp85Asn) AND not provided ClinVar Detail
NM_000219.6(KCNE1):c.253G>A (p.Asp85Asn) AND Long QT syndrome ClinVar Detail
NM_000219.6(KCNE1):c.253G>A (p.Asp85Asn) AND Cardiovascular phenotype ClinVar Detail
NM_000219.6(KCNE1):c.253G>A (p.Asp85Asn) AND Jervell and Lange-Nielsen syndrome 2 ClinVar Detail
NM_000219.6(KCNE1):c.253G>A (p.Asp85Asn) AND Long QT syndrome 5 ClinVar Detail
NM_000219.6(KCNE1):c.253G>A (p.Asp85Asn) AND Cardiomyopathy ClinVar Detail
NM_000219.6(KCNE1):c.253G>A (p.Asp85Asn) AND Congenital long QT syndrome ClinVar Detail
NM_000219.6(KCNE1):c.253G>A (p.Asp85Asn) AND multiple conditions ClinVar Detail
NM_000219.6(KCNE1):c.253G>A (p.Asp85Asn) AND multiple conditions ClinVar Detail
NA DisGeNET Detail
Screening the family members for three LQTS modifiers (rs4657139 and rs16847548 in NOS1AP and KCNE1-... DisGeNET Detail
Screening the family members for three LQTS modifiers (rs4657139 and rs16847548 in NOS1AP and KCNE1-... DisGeNET Detail
Genetic screening identified a KCNE1 D85N variant, which has been reported to be a LQTS-causing gene... DisGeNET Detail
During the tachycardia phase following adenosine, QTc increased to 620 ms. Genetic analysis revealed... DisGeNET Detail
Instability of KCNE1-D85N that causes long QT syndrome: stabilization by verapamil. DisGeNET Detail
NA DisGeNET Detail
D85N, a KCNE1 polymorphism, is a disease-causing gene variant in long QT syndrome. DisGeNET Detail
Drug-induced QT-interval prolongation and recurrent torsade de pointes in a child with heterotaxy sy... DisGeNET Detail
The common KCNE1 D85N potassium channel variant prolongs QT interval by inhibiting IKs (KCNQ1) and I... DisGeNET Detail
Screening of the genotype disclosed the KCNE1 D85N polymorphism, which is known as one of the typica... DisGeNET Detail
The common KCNE1 D85N potassium channel variant prolongs QT interval by inhibiting IKs (KCNQ1) and I... DisGeNET Detail
Aborted cardiac arrest in a patient carrying KCNE1 D85N variant during the postpartum period. DisGeNET Detail
A large candidate gene survey identifies the KCNE1 D85N polymorphism as a possible modulator of drug... DisGeNET Detail
KCNE1 D85N polymorphism--a sex-specific modifier in type 1 long QT syndrome? 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
rs1805128 dbSNP
Genome
hg38
Position
chr21:34,449,382-34,449,382
Variant Type
snv
Reference Allele
C
Alternative Allele
T
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
80.60
Standard deviation of sample read depth (HGVD)
42.14
Number of reference allele (HGVD)
2384
Number of alternative allele (HGVD)
36
Allele Frequency (HGVD)
0.01487603305785124
Gene Symbol (HGVD)
KCNE1
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))
rs1805128
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0113
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
189
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8636
East Asian Allele Counts (ExAC)
48
East Asian Heterozygous Counts (ExAC)
48
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.00555812876331635
Chromosome Counts in All Race (ExAC)
121208
Allele Counts in All Race (ExAC)
1110
Heterozygous Counts in All Race (ExAC)
1098
Homozygous Counts in All Race (ExAC)
6
Allele Frequency in All Race (ExAC)
0.00915781136558643
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