KCNQ1 Variant R539W Detail

We estimate the penetrance of LQTS for KCNQ1 R539W is 71%. This variant was found in a total of 28 carriers in 13 papers or gnomAD, 21 had LQTS. R539W is present in 1 alleles in gnomAD. R539W has been functionally characterized in 1 papers. This residue is located in a Hotspot region for LQT1. In silico predictions, functional data (if available), and location in structure are equivalent to observing 6 individuals with LQT1 and 4 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 R539W around 71% (27/38).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-6.6 1.0 -3 0.94 69
PROVEAN scores less than -2 are considered deleterious. REVEL scores higher than 0.5 or 0.75 are considered likely pathogenic (higher sensitivity with the former cutoff, higher specificity with the latter cutoff). A PolyPhen-2 score of 0.85 or greater is considered likely pathogenic. BLAST-PSSM reflects the evolutionary conservation of residue substitutions, more negative numbers indicate fewer observations of the specific substitution than is expected. Penetrance density is our previously published method to calculate the average LQTS probability density in a shell of residues surrounding a residue of interest (Kroncke et al. 2019).

Reported Carrier Data

PubMed ID Year Carriers Unaffected LQT1 Other Disease
32893267 2020 12 None 12 None
30758498 2019 3 None 1 None
29688407 2018 1 1 None None
24681627 2014 None None None None
24218437 2013 1 None 1 None
23631430 2013 3 None None None
22949429 2012 6 None 6 None
19841300 2009 6 None 6 None
19716085 2009 6 None 6 None
17192539 2006 1 None 1 None
15746441 2005 None None None None
14678125 2003 2 None 2 None
10728423 2000 7 5 2 None
Summary totals might not agree with the literature table because of duplicate patients, which were excluded from the total counts. We do not distinguish here between multiple missense codons. Missense variants are combined across degenerate codon substitutions since codon-level data were not consistently available for curation.

Functional Data Homozygously Collected

Peak current is relative to wildtype (100% being no different from wildtype). V0.5 activation is the voltages at which half of the maximal current is reached during an activation in units of mV and relative to wildtype. Recovery from inactivation (Rec. inact.) and deactivation time (Deactivation) are the ratio of characteristic time constants with wildtype (unitless).

PubMed ID Cell Type Peak Current IKs (%WT) V1/2 Act. Activation time (%WT) Deactivation time (%WT)
10728423 COS 17 33.9 1.0 0.40990991

Functional Data Heterozygously Collected

Functional parameters are the same as defined above.

PubMed ID Cell Type Peak Current IKs (%WT) V1/2 Act. Activation time (%WT) Deactivation time (%WT)
10728423 COS 55 22.5 1.0 0.681538462

R539W has 15 previously observed neighbors within 15 angstroms

A residue within a folded protein on average has nearest neighbors that fall roughly into two shells: a "nearest" neighbor around 5-6 angstroms and a second shell around 11 angstroms. NOTE: some residues appear multiple times at different distances. This results from the fact that the functional KV7.1 channel is a homotetramer and occasionally the same residue from multiple subunits is present within the 15A window. All variants shown in the rightmost column have been observed in at least one individual in the literature or gnomAD.

Neighbor Distance (Angstroms) Variants Observed in Individuals
538 11
362 11 K362R, K362del,
537 12
531 12
541 12 V541I,
534 12
539 13 R539W, R539L, R539Q,
536 13
361 13
532 13
540 14
366 14 R366W, R366Q,
360 14 R360ins, R360G, R360M,
542 14
527 15