KCNQ1 Variant V294M Detail

We estimate the penetrance of LQTS for KCNQ1 V294M is 12%. This variant was found in a total of 4 carriers in 0 papers or gnomAD, 0 had LQTS. V294M is present in 4 alleles in gnomAD. V294M has not been functionally characterized. This residue is located in a Mild_Hotspot region for LQT1. In silico predictions, functional data (if available), and location in structure are equivalent to observing 1 individuals with LQT1 and 9 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 V294M around 12% (1/14).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-0.49 0.1 -1 0.604 15
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
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.

V294M has 26 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
294 0 V294M,
297 5 G297S, G297D, G297R,
296 7 F296S, F296L, F296L, F296L,
285 8
286 8
298 9 S298I, S298N,
301 9
281 10 Y281C,
293 11 R293C, R293H,
302 11 A302V, A302E, A302T,
283 12 A283G, A283T,
300 12 A300T, A300S,
280 12 V280A, V280E,
144 13 T144A,
290 13 E290K,
146 13 E146K, E146G, E146Q,
145 13
305 13 W305S, W305L, W305C, W305C, W305R, W305R,
299 13
321 13
317 14 D317N, D317G, D317Y,
318 14
282 14 L282P,
289 14
288 15
303 15 L303P,