KCNH2 Variant K434N Detail

We estimate the penetrance of LQTS for KCNH2 K434N is 14%. We are unaware of any observations of this variant in individuals. K434N is not present in gnomAD. K434N has not been functionally characterized. This residue is located in a Mild_Hotspot region for LQT2. In silico predictions, functional data (if available), and location in structure are equivalent to observing 1 individuals with LQT2 and 9 unaffected individuals.These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 K434N around 14% (1/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
2.251 0.004 4 0.481 27
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 LQT2 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.

K434N 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 since the functional KV11.1 channel (protein product of KCNH2/hERG) 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
434 0
433 4
435 4 E435X, E435G,
432 5
436 5 T436M,
431 7 F431L, F431L, F431L,
437 7
430 8
438 8 E438X, E438K,
429 8 A429V, A429P,
439 8
428 9 S428L, S428fsX, S428X,
440 9 P440L,
427 10 Y427H, Y427C, Y427S,
441 10 P441R, P441L,
426 11 P426H,
442 11
425 11
443 11 T443fsX, T443N,
424 12
444 12 E444D, E444D, E444K,
423 13
445 13
422 13 A422T,
446 13
421 14 T421fsX, T421M,
447 14 Y447X,
420 14 Y420C,
448 14 A448S, A448T,
419 15
449 15