rs199472681
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_000218.3(KCNQ1):c.365G>A(p.Cys122Tyr) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: not found (cov: 32)
Consequence
KCNQ1
NM_000218.3 missense
NM_000218.3 missense
Scores
13
4
1
Clinical Significance
Conservation
PhyloP100: 6.93
Genes affected
KCNQ1 (HGNC:6294): (potassium voltage-gated channel subfamily Q member 1) This gene encodes a voltage-gated potassium channel required for repolarization phase of the cardiac action potential. This protein can form heteromultimers with two other potassium channel proteins, KCNE1 and KCNE3. Mutations in this gene are associated with hereditary long QT syndrome 1 (also known as Romano-Ward syndrome), Jervell and Lange-Nielsen syndrome, and familial atrial fibrillation. This gene exhibits tissue-specific imprinting, with preferential expression from the maternal allele in some tissues, and biallelic expression in others. This gene is located in a region of chromosome 11 amongst other imprinted genes that are associated with Beckwith-Wiedemann syndrome (BWS), and itself has been shown to be disrupted by chromosomal rearrangements in patients with BWS. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
PM1
?
In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 9 uncertain in NM_000218.3
PM2
?
Very rare variant in population databases, with high coverage;
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.987
PP5
?
Variant 11-2445463-G-A is Pathogenic according to our data. Variant chr11-2445463-G-A is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 53039.We mark this variant Likely_pathogenic, oryginal submissions are: {not_provided=1, Pathogenic=1, Uncertain_significance=1}. Variant chr11-2445463-G-A is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNQ1 | NM_000218.3 | c.365G>A | p.Cys122Tyr | missense_variant | 1/16 | ENST00000155840.12 | |
KCNQ1 | NM_001406837.1 | c.3G>A | p.Met1? | start_lost | 1/17 | ||
KCNQ1 | NM_001406836.1 | c.365G>A | p.Cys122Tyr | missense_variant | 1/15 | ||
KCNQ1 | NM_001406838.1 | c.365G>A | p.Cys122Tyr | missense_variant | 1/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNQ1 | ENST00000155840.12 | c.365G>A | p.Cys122Tyr | missense_variant | 1/16 | 1 | NM_000218.3 | P1 | |
KCNQ1 | ENST00000345015.4 | n.142G>A | non_coding_transcript_exon_variant | 1/3 | 1 | ||||
KCNQ1 | ENST00000496887.7 | c.104G>A | p.Cys35Tyr | missense_variant | 2/16 | 5 | |||
KCNQ1 | ENST00000646564.2 | c.365G>A | p.Cys122Tyr | missense_variant | 1/11 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:1Other:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Nov 26, 2013 | p.Cys122Tyr (TGC>TAC): c.365 G>A in exon 1 of the KCNQ1 gene (NM_000218.2). The Cys122Tyr mutation in the KCNQ1 gene has been reported in association with LQTS and Jervell and Lange-Nielson syndrome (JLNS) (Tester D et al., 2005; Giudicessi et al., 2012; Giudicessi et al., 2013). Tester et al. and Giudicessi et al. (2012) each reported Cys122Tyr in an individual with LQTS and it was absent from more than 1,500 control alleles. Giudicessi et al. (2013) identified Cys122Tyr in a patient, who harbored another mutation in the KCNQ1 gene, with a history of deafness and LQTS. Cys122Tyr was inherited from an asymptomatic mother. Cys122Tyr results in a conservative amino acid substitution of one neutral, polar amino acid with another at a position that is conserved across species. Furthermore, the Cys122Tyr mutation was not observed inapproximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. In summary, Cys122Tyr in the KCNQ1 gene is interpreted as a disease-causing mutation. The variant is found in LQT panel(s). - |
Long QT syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Apr 25, 2019 | In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This variant has been reported to affect KCNQ1 protein function (PMID: 29532034). This variant has been observed with a second variant in KCNQ1 in an individual affected with Jervell and Lange-Nielsen syndrome (PMID: 23392653). ClinVar contains an entry for this variant (Variation ID: 53039). This variant is not present in population databases (ExAC no frequency). This sequence change replaces cysteine with tyrosine at codon 122 of the KCNQ1 protein (p.Cys122Tyr). The cysteine residue is highly conserved and there is a large physicochemical difference between cysteine and tyrosine. - |
Congenital long QT syndrome Other:1
not provided, no classification provided | literature only | Cardiovascular Biomedical Research Unit, Royal Brompton & Harefield NHS Foundation Trust | - | This variant has been reported as associated with Long QT syndrome in the following publications (PMID:15840476;PMID:19841300). This is a literature report, and does not necessarily reflect the clinical interpretation of the Imperial College / Royal Brompton Cardiovascular Genetics laboratory. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
CardioboostArm
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Pathogenic
D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Pathogenic
D
MutationTaster
Benign
D
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
D;D;.
REVEL
Pathogenic
Sift
Uncertain
D;D;.
Sift4G
Pathogenic
D;D;.
Polyphen
0.99
.;D;.
Vest4
0.96
MutPred
0.92
.;Loss of methylation at K121 (P = 0.027);.;
MVP
MPC
2.8
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at