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.296C>G (p.Pro99Arg)

CA006767

200877 (ClinVar)

Gene: KCNQ1
Condition: long QT syndrome 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 2cf0981a-860e-4d2d-93c7-21a514d8de32
Approved on: 2025-07-01
Published on: 2025-07-02

HGVS expressions

NM_000218.3:c.296C>G
NM_000218.3(KCNQ1):c.296C>G (p.Pro99Arg)
NC_000011.10:g.2445394C>G
CM000673.2:g.2445394C>G
NC_000011.9:g.2466624C>G
CM000673.1:g.2466624C>G
NC_000011.8:g.2423200C>G
NG_008935.1:g.5404C>G
ENST00000496887.7:c.35C>G
ENST00000646564.2:c.296C>G
ENST00000155840.12:c.296C>G
ENST00000155840.9:c.296C>G
ENST00000345015.4:n.73C>G
ENST00000496887.6:c.35C>G
NM_000218.2:c.296C>G
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Uncertain Significance

Met criteria codes 1
PP3
Not Met criteria codes 16
PS2 PS4 PS3 PS1 BA1 PP4 PP1 PM6 PM2 PM1 PM5 BS4 BS3 BS1 BP5 BP4

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.296C>G is a missense variant predicted to cause replacement of proline with arginine at position 99. This variant is present in gnomAD v.4.1.0 at a maximum allele frequency of 0.0001201, with 9/74916 in the African / African-American population, which is higher than the ClinGen Potassium Channel Arrhythmia VCEP PM2_Supporting threshold of <0.00001, but lower than the BS1 threshold of >0.0004, so neither criterion is met. This variant is rare and has been reported in 1 proband affected with heart murmur and sudden infant death during sleep, however, QTc interval is not available and the requirement for 2 unrelated probands has not been reached so the PS4_Supporting code is not yet met (PMID: 24631775). The computational predictor REVEL gives a score of 0.861, which is above the ClinGen Potassium Channel Arrhythmia VCEP PP3 threshold of >0.75 and predicts a damaging effect on KCNQ1 function (PP3). 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: PP3. (VCEP specifications version 1.0.0; date of approval 03/04/2025).
Met criteria codes
PP3
Met at supporting level with REVEL = 0.861 (>0.75).
Not Met criteria codes
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
This variant is rare and has been reported in 1 proband affected with heart murmur and sudden infant death during sleep, however, QTc interval is not available and the requirement for 2 unrelated probands has not been reached so the PS4_Supporting code is not yet met (PMID: 24631775).
PS3
No experimental studies available.
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BA1
The maximum allele frequency does not exceed 0.4% in any of the 5 continental subpopulations in gnomAD.
PP4
The only documented patient had the non-specific phenotype of sudden infant death/sudden unexpected death.
PP1
No cases with genetic testing of family members are available.
PM6
The proband has a presumed de novo variant with a phenotype that is consistent with the gene but the sudden unexpected death (SUD) phenotype is not highly specific and has high genetic heterogeneity (=0.25), which is insufficient to meet criteria for PM6.
PM2
This variant is present in gnomAD v.4.1.0 at a maximum allele frequency of 0.0001201, with 9/74916 in the African / African-American population, which is higher than the ClinGen Potassium Channel Arrhythmia VCEP PM2_Supporting threshold of <0.00001, but lower than the BS1 threshold of >0.0004, so neither criterion is met.
PM1
Not applicable as PM2 is not met. Additionally, variant is not in the pore helix (amino acids 300 to 320).
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No cases with genetic testing of family members are available.
BS3
No experimental studies available.
BS1
The maximum allele frequency in the gnomAD 5 continental subpopulations of 0.012% (African, gnomAD 4) does not exceed 0.04%.
BP5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
SpliceAI delta scores are all zero however this code is not met as REVEL = 0.861 (>0.25).
Curation History
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