KCNQ1 Variant S402R Detail

We estimate the penetrance of LQTS for KCNQ1 S402R is 23%. We are unaware of any observations of this variant in individuals. S402R is not present in gnomAD. S402R 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 2 individuals with LQT1 and 8 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 S402R around 23% (2/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-0.7 0.002 -1 0.628 28
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: - 0 0 0
VARIANT FEATURES ALONE: - 10 8 2 -
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.

S402R 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
402 0
401 4 R401W, R401Q,
403 4 H403P,
400 5
404 5
399 7 A399S, A399V, A399G,
405 7
398 8 K398R,
406 8
397 8 R397W, R397Q, R397G,
407 8
396 9
408 9 P408A,
395 10 Y395C,
409 10
394 11 I394L,
410 11
393 11 K393N,
411 11
392 12 W392R, W392R, W392ins,
412 12 P412S,
391 13 T391A, T391I,
413 13 K413R,
390 13
414 13
389 14 S389P,
415 14
388 14 D388H, D388N,
416 14 V416M,
387 15 P387T,
417 15 V417M,