The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000218.3(KCNQ1):c.565G>A (p.Gly189Arg)

CA007480

3114 (ClinVar)

Gene: KCNQ1
Condition: long QT syndrome 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 34eb77d3-738e-4afe-8242-6c6c160ee61a
Approved on: 2025-07-01
Published on: 2025-07-02

HGVS expressions

NM_000218.3:c.565G>A
NM_000218.3(KCNQ1):c.565G>A (p.Gly189Arg)
NC_000011.10:g.2570715G>A
CM000673.2:g.2570715G>A
NC_000011.9:g.2591945G>A
CM000673.1:g.2591945G>A
NC_000011.8:g.2548521G>A
NG_008935.1:g.130725G>A
ENST00000496887.7:c.304G>A
ENST00000646564.2:c.478-12720G>A
ENST00000155840.12:c.565G>A
ENST00000335475.6:c.184G>A
ENST00000646564.1:c.124-12720G>A
ENST00000155840.9:c.565G>A
ENST00000335475.5:c.184G>A
ENST00000496887.6:c.304G>A
NM_000218.2:c.565G>A
NM_181798.1:c.184G>A
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Uncertain Significance

Met criteria codes 4
PS4_Supporting PP3 PM2_Supporting PS3_Moderate
Not Met criteria codes 1
PP1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Potassium Channel Arrhythmia Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for KCNQ1 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Potassium Channel Arrhythmia VCEP
NM_000218.3(KCNQ1):c.565G>A (p.Gly189Arg) is a missense variant that causes replacement of glycine with arginine at position 189. This variant is present in gnomAD v.4.1.0 at a maximum allele frequency of 0.00002228, with 1/44884 in the East Asian population, which is lower than the ClinGen Potassium Channel Arrhythmia VCEP PM2_Supporting threshold of <0.00001 (PM2_Supporting). This variant is rare and has been reported in at least 2 apparently unrelated probands affected with long QT syndrome 1 (PS4_Supporting, PMID: 8528244, PMID: 10220144, PMID: 17470695). The computational predictor REVEL gives a score of 0.967, which is above the ClinGen Potassium Channel Arrhythmia VCEP PP3 threshold of >0.75 and predicts a damaging effect on KCNQ1 function. The computational splicing predictor SpliceAI gives a score of 0.43 for donor loss, which is lower than the ClinGen Potassium Channel Arrhythmia VCEP threshold of >0.5 and does not strongly predict that the variant disrupts the splicing of KCNQ1 (PP3). This variant has been shown to disrupt KCNQ1 function in three experimental assays, including manual patch-clamp, particularly in its impaired activation by treatment with the adenylyl cyclase / protein kinase A activator forskolin, and experimental / structural / functional simulation (PS3_Moderate; PMID: 22456477, PMID: 10376919, PMID: 29021305). In summary, this variant meets the criteria to be classified as a variant of uncertain significance for long QT syndrome 1 based on the ACMG/AMP criteria applied, as specified by the ClinGen Potassium Channel Arrhythmia VCEP: PS3_Moderate, PS4_Supporting, PM2_Supporting, and PP3. (VCEP specifications version 1.0.0; date of approval 03/04/2025).
Met criteria codes
PS4_Supporting
This variant is rare and has been reported in at least 2 apparently unrelated probands affected with long QT syndrome 1 (PS4_Supporting, PMID: 8528244, PMID: 10220144, PMID: 17470695).
PP3
The computational predictor REVEL gives a score of 0.967, which is above the ClinGen Potassium Channel Arrhythmia VCEP PP3 threshold of >0.75 and predicts a damaging effect on KCNQ1 function. The computational splicing predictor SpliceAI gives a score of 0.43 for donor loss, which is lower than the ClinGen Potassium Channel Arrhythmia VCEP threshold of >0.5 and does not strongly predict that the variant disrupts the splicing of KCNQ1 (PP3).
PM2_Supporting
This variant is present in gnomAD v.4.1.0 at a maximum allele frequency of 0.00002228, with 1/44884 in the East Asian population, which is lower than the ClinGen Potassium Channel Arrhythmia VCEP PM2_Supporting threshold of <0.00001 (PM2_Supporting).
PS3_Moderate
This variant has been shown to disrupt KCNQ1 function in three experimental assays, including manual patch-clamp, particularly in its impaired activation by treatment with the adenylyl cyclase / protein kinase A activator forskolin, and experimental / structural / functional simulation (PS3_Moderate; PMID: 22456477, PMID: 10376919, PMID: 29021305).
Not Met criteria codes
PP1
The variant has been reported to segregate with long QT syndrome 1 through the proband and multiple affected family members in two different families, however, the available phenotype details are not sufficient to meet PP1 (PMID: 22373669, PMID: 8528244).
Curation History
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