KCNQ1 Variant W305C Detail

We estimate the penetrance of LQTS for KCNQ1 W305C is 79%. This variant was found in a total of 3 carriers in 1 papers or gnomAD, 3 had LQTS. W305C is not present in gnomAD. W305C has not been functionally characterized. 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 7 individuals with LQT1 and 3 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 W305C around 79% (10/13).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-12.65 1.0 0 0.973 83
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
19490272 2009 3 None 3 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.

W305C has 19 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
326 11
314 12 G314S, G314D, G314C, G314del,
281 12 Y281C,
330 12
316 13 G316E, G316R, G316R, G316V,
325 13 G325R, G325R, G325E, G325W,
274 13 I274V,
272 14 G272D, G272S, G272V,
315 14 Y315C, Y315S, Y315N, Y315H, Y315F,
319 14 V319L, V319L,
313 14
327 14 T327A, T327S, T327S,
278 14 Y278H,
328 14 I328del,
322 14 T322M, T322A, T322K,
312 14 T312del, T312I,
284 15 E284K,
282 15 L282P,
309 15 T309I, T309R,