rs1435990592
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_000218.3(KCNQ1):c.200_210del(p.Pro67ArgfsTer214) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 8.0e-7 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
KCNQ1
NM_000218.3 frameshift
NM_000218.3 frameshift
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.827
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 Pathogenic. Variant got 18 ACMG points.
PVS1
?
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 11-2445294-TCCCCGGCCGCG-T is Pathogenic according to our data. Variant chr11-2445294-TCCCCGGCCGCG-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 449221.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr11-2445294-TCCCCGGCCGCG-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
KCNQ1 | NM_000218.3 | c.200_210del | p.Pro67ArgfsTer214 | frameshift_variant | 1/16 | ENST00000155840.12 | |
KCNQ1 | NM_001406836.1 | c.200_210del | p.Pro67ArgfsTer214 | frameshift_variant | 1/15 | ||
KCNQ1 | NM_001406838.1 | c.200_210del | p.Pro67ArgfsTer212 | frameshift_variant | 1/11 | ||
KCNQ1 | NM_001406837.1 | c.-163_-153del | 5_prime_UTR_variant | 1/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
KCNQ1 | ENST00000155840.12 | c.200_210del | p.Pro67ArgfsTer214 | frameshift_variant | 1/16 | 1 | NM_000218.3 | P1 | |
KCNQ1 | ENST00000646564.2 | c.200_210del | p.Pro67ArgfsTer212 | frameshift_variant | 1/11 | ||||
KCNQ1 | ENST00000496887.7 | c.24-85_24-75del | intron_variant | 5 | |||||
KCNQ1 | ENST00000345015.4 | upstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 8.03e-7 AC: 1AN: 1244822Hom.: 0 AF XY: 0.00000164 AC XY: 1AN XY: 610262
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
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1
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1244822
Hom.:
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1
AN XY:
610262
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GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
Bravo
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ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:8
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Pathogenic:3
Pathogenic, no assertion criteria provided | provider interpretation | Stanford Center for Inherited Cardiovascular Disease, Stanford University | Oct 12, 2016 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Jun 03, 2021 | Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Identified in patients with Long QT syndrome referred for testing at GeneDx and in the published literature (Kapplinger et al., 2009).; Not observed at significant frequency in large population cohorts (Lek et al., 2016) This variant is associated with the following publications: (PMID: 19716085, 27535533, 26582918) - |
Pathogenic, criteria provided, single submitter | clinical testing | AiLife Diagnostics, AiLife Diagnostics | Dec 30, 2021 | - - |
Long QT syndrome 1 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Molecular Genetics Laboratory - Cardiogenetics, CHU de Nantes | Aug 01, 2023 | - - |
Beckwith-Wiedemann syndrome;C1837014:Atrial fibrillation, familial, 3;C1865019:Short QT syndrome type 2;C4551509:Jervell and Lange-Nielsen syndrome 1;C4551647:Long QT syndrome 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Dec 05, 2021 | - - |
KCNQ1-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Jan 26, 2024 | The KCNQ1 c.200_210del11 variant is predicted to result in a frameshift and premature protein termination (p.Pro67Argfs*214). This variant has been reported to be causative for long QT syndrome (described as 200_210delCGGCCGCGCCC (S66fs+213X) in Table S1, Kapplinger et al. 2009. PubMed ID: 19716085). This variant has not been reported in a large population database, indicating this variant is rare. Frameshift variants in KCNQ1 are expected to be pathogenic. This variant is interpreted as pathogenic. - |
Long QT syndrome Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jul 07, 2023 | This sequence change creates a premature translational stop signal (p.Pro67Argfs*214) 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 not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with long QT syndrome (PMID: 19716085). ClinVar contains an entry for this variant (Variation ID: 449221). For these reasons, this variant has been classified as Pathogenic. - |
Cardiovascular phenotype Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 13, 2018 | The c.200_210del11 pathogenic mutation, located in coding exon 1 of the KCNQ1 gene, results from a deletion of 11 nucleotides at nucleotide positions 200 to 210, causing a translational frameshift with a predicted alternate stop codon (p.P67Rfs*214). In a study of long QT syndrome clinical genetic testing, this alteration (also described as S66fs+213X) was reported in one patient; however, clinical details were limited (Kapplinger JD et al. Heart Rhythm, 2009 Sep;6:1297-303). In addition to the clinical data presented in the literature, 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
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at