KCNQ1 Variant N429S Detail

We estimate the penetrance of LQTS for KCNQ1 N429S is 9%. This variant was found in a total of 2 carriers in 0 papers or gnomAD, 0 had LQTS. N429S is present in 2 alleles in gnomAD. N429S has not been functionally characterized. This residue is located in a Non_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 N429S around 9% (1/12).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-1.5 0.029 0 0.489 1
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
LITERATURE, COHORT, AND GNOMAD: - 2 2 0
VARIANT FEATURES ALONE: - 10 9 1 -
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.

N429S has 31 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
429 0 N429S,
428 4 D428G,
430 4
427 5
431 5 V431L, V431L,
426 7
432 7 T432I, T432A,
425 8 L425V,
433 8 P433A,
424 8 K424T,
434 8 G434R, G434R,
423 9
435 9
422 10 K422T, K422R,
436 10
421 11 K421N, K421N,
437 11 M437V,
420 11 K420E, K420N, K420N,
438 11
419 12
439 12
418 13 V418I,
440 13
417 13 V417M,
441 13 P441S,
416 14 V416M,
442 14 H442R,
415 14
443 14
414 15
444 15 T444M, T444K,