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.958C>T (p.Pro320Ser)

CA008910

67130 (ClinVar)

Gene: KCNQ1
Condition: long QT syndrome 1
Inheritance Mode: Autosomal dominant inheritance
UUID: bd615d9c-f6ab-4dfc-ac84-670e9fc3918b
Approved on: 2025-07-01
Published on: 2025-07-02

HGVS expressions

NM_000218.3:c.958C>T
NM_000218.3(KCNQ1):c.958C>T (p.Pro320Ser)
NC_000011.10:g.2583471C>T
CM000673.2:g.2583471C>T
NC_000011.9:g.2604701C>T
CM000673.1:g.2604701C>T
NC_000011.8:g.2561277C>T
NG_008935.1:g.143481C>T
ENST00000496887.7:c.697C>T
ENST00000646564.2:c.514C>T
ENST00000155840.12:c.958C>T
ENST00000335475.6:c.577C>T
ENST00000646564.1:c.160C>T
ENST00000155840.9:c.958C>T
ENST00000335475.5:c.577C>T
NM_000218.2:c.958C>T
NM_181798.1:c.577C>T
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Uncertain Significance

Met criteria codes 4
PP3 PM2_Supporting PM1 PS4_Supporting
Not Met criteria codes 6
BP4 PS3 PP1 PM5 BA1 BS1

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.958C>T is a missense variant predicted to cause substitution of proline by serine at amino acid 320 (p.Pro320Ser). This variant is rare and has been reported in 2 apparently unrelated probands affected with long QT syndrome 1 (PS4_Supporting; PMID: 23392653, PMID: 32383558). This variant is absent in gnomAD v.2.1.1, but present in gnomAD v4.1.0 at a maximum allele frequency of 0.0000008994, with 1 allele / 1,111,812 total alleles in the European Non-Finnish population, which is lower than the ClinGen Potassium Channel Arrhythmia VCEP PM2_Supporting threshold of <0.00001 (PM2_Supporting). This variant is a missense substitution within the pore helix consisting of amino acids 300 to 320, which is a well-characterized functional domain required for the channel function and selectivity filter of KCNQ1 (PMID: 15649981), and has been confirmed to show an absence of likely benign or benign variants listed in gnomAD (PM1). The computational predictor REVEL gives a score of 0.98, 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 due to insufficient evidence for long QT syndrome 1 based on the ACMG/AMP criteria applied, as specified by the ClinGen Potassium Channel Arrhythmia VCEP: PS4_Supporting, PM2_Supporting, PM1, PP3. (VCEP specifications version 1.0.0; date of approval 03/04/2025).
Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.98, which is above the ClinGen Potassium Channel Arrhythmia VCEP PP3 threshold of >0.75 and predicts a damaging effect on KCNQ1 function (PP3).
PM2_Supporting
This variant is absent in gnomAD v.2.1.1, but present in gnomAD v4.0.0 at a maximum allele frequency of 8.994e-7, with 1 allele/1111812 total alleles in the European Non-Finnish population, which is lower than the ClinGen Potassium Channel Arrhythmia VCEP PM2_Supporting threshold of <0.00001 (PM2_Supporting).
PM1
This variant is a missense substitution within the pore helix consisting of amino acids 300 to 320, which is a well-characterized functional domain required for the channel function and selectivity filter of KCNQ1 (PMID: 15649981), and has been confirmed to show an absence of likely benign or benign variants listed in gnomAD (PM1).
PS4_Supporting
This variant is rare and has been reported in 2 apparently unrelated probands affected with long QT syndrome 1 (PS4_Supporting; PMID: 23392653, PMID: 32383558).
Not Met criteria codes
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
This variant has been shown to disrupt KCNQ1 function in one experimental assay, Experimental Functional Simulation (PMID 35442947), but has not yet been reported in other functional studies to meet PS3 at any level.
PP1
Six family members carry this variant, but none with enough clinical detail to count (PMID: 23392653).
PM5
Another missense variant in the same codon, c.959C>A (p.Pro320His), has been classified as likely pathogenic for long QT syndrome 1 by the ClinGen Potassium Channel Arrhythmia VCEP, while no benign missense variants have been identified in this codon. This residue has been confirmed to be highly conserved across all 5 human KCNQ paralogues, and SpliceAI has been used to confirm that neither variant has a predicted impact on KCNQ1 splicing. Not scoring this data for PM5 so as not to double-count with PM1.
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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