rs397508109
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PVS1PP5_Very_Strong
The NM_000218.3(KCNQ1):c.364dup(p.Cys122LeufsTer163) variant causes a frameshift change. The variant allele was found at a frequency of 0.0000144 in 1,596,406 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. K121K) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_000218.3 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNQ1 | NM_000218.3 | c.364dup | p.Cys122LeufsTer163 | frameshift_variant | 1/16 | ENST00000155840.12 | |
KCNQ1 | NM_001406836.1 | c.364dup | p.Cys122LeufsTer163 | frameshift_variant | 1/15 | ||
KCNQ1 | NM_001406838.1 | c.364dup | p.Cys122LeufsTer161 | frameshift_variant | 1/11 | ||
KCNQ1 | NM_001406837.1 | c.2dup | p.Met1? | frameshift_variant, start_lost | 1/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNQ1 | ENST00000155840.12 | c.364dup | p.Cys122LeufsTer163 | frameshift_variant | 1/16 | 1 | NM_000218.3 | P1 | |
KCNQ1 | ENST00000345015.4 | n.141dup | non_coding_transcript_exon_variant | 1/3 | 1 | ||||
KCNQ1 | ENST00000496887.7 | c.103dup | p.Cys35LeufsTer163 | frameshift_variant | 2/16 | 5 | |||
KCNQ1 | ENST00000646564.2 | c.364dup | p.Cys122LeufsTer161 | frameshift_variant | 1/11 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000227 AC: 5AN: 219922Hom.: 0 AF XY: 0.0000409 AC XY: 5AN XY: 122282
GnomAD4 exome AF: 0.0000152 AC: 22AN: 1444266Hom.: 0 Cov.: 31 AF XY: 0.0000278 AC XY: 20AN XY: 718768
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74326
ClinVar
Submissions by phenotype
Long QT syndrome 1 Pathogenic:3
Likely pathogenic, criteria provided, single submitter | clinical testing | Arcensus | Feb 01, 2013 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Centre for Mendelian Genomics, University Medical Centre Ljubljana | Aug 12, 2019 | This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS1,PP4. - |
Pathogenic, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 04, 2015 | - - |
KCNQ1-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jul 10, 2023 | The KCNQ1 c.364dupT variant is predicted to result in a frameshift and premature protein termination (p.Cys122Leufs*163). This variant has been reported in multiple individuals with long QT syndrome in both the heterozygous and homozygous state (described as InsG 2025-2026 K121fs/629* in Tester et al. 2005. PubMed ID: 15840476; Schwartz et al. 2021. PubMed ID: 34505893; described as c.365insT in Kapplinger et al. 2009. PubMed ID: 19716085; Whiffin et al. 2019. PubMed ID: 30609406; Jacobson et al. 2014. PubMed ID: 24665220). This variant is reported in 0.017% of alleles in individuals of South Asian descent in gnomAD (http://gnomad.broadinstitute.org/variant/11-2466691-A-AT). Frameshift variants in KCNQ1 are expected to be pathogenic. This variant is interpreted as pathogenic. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | May 08, 2017 | The c.364dupT pathogenic variant in the KCNQ1 gene (also reported as K121fs+162X, 365insT, Ins G 2025-2026, and K121fs/629 due to alternative nomenclature) has previously been reported in individuals referred for LQTS genetic testing (Tester et al., 2005; Kapplinger et al., 2009). The c.364dupT variant causes a shift in reading frame starting at codon cysteine 122, changing it to a leucine, and creating a premature stop codon at position 163 of the new reading frame, denoted p.Cys122LeufsX163. This pathogenic variant is expected to result in either an abnormal, truncated protein product or loss of protein from this allele through nonsense-mediated mRNA decay. Other downstream frameshift variants in the KCNQ1 gene have been reported in Human Gene Mutation Database in association with LQTS and JLNS (Stenson et al., 2014), indicating that loss of function is a mechanism of disease for this gene. Furthermore, the c.364dupT variant has not been observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). - |
Long QT syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 13, 2024 | This sequence change creates a premature translational stop signal (p.Cys122Leufs*163) in the KCNQ1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in KCNQ1 are known to be pathogenic (PMID: 9323054, 19862833). This variant is present in population databases (rs397508109, gnomAD 0.02%). This premature translational stop signal has been observed in individual(s) with clinical features of long QT syndrome (PMID: 15840476). This variant is also known as Ins G 2025-2026 (K121fs/629*). ClinVar contains an entry for this variant (Variation ID: 200915). For these reasons, this variant has been classified as Pathogenic. - |
Cardiovascular phenotype Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 18, 2019 | The c.364dupT pathogenic mutation, located in coding exon 1 of the KCNQ1 gene, results from a duplication of T at nucleotide position 364, causing a translational frameshift with a predicted alternate stop codon (p.C122Lfs*163). This alteration has been detected in the homozygous state in a child of consanguineous parents who was reported to have Jervell and Lange-Nielsen syndrome. The parents were reported to have normal ECGs (Jacobson D et al. Paediatr Child Health, 2014 Mar;19:123-4). This alteration (also referred to as K121fs/629* and 365insT) has also been detected in long QT syndrome genetic testing cohorts; however, details were limited (Tester DJ et al. Heart Rhythm, 2005 May;2:507-17; Kapplinger JD et al. Heart Rhythm, 2009 Sep;6:1297-303). This alteration is expected to result in loss of function by premature protein truncation or nonsense-mediated mRNA decay. As such, this alteration is interpreted as a disease-causing mutation. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at