KCNH2 Variant G439C Detail

We estimate the penetrance of LQTS for KCNH2 G439C is 11%. We are unaware of any observations of this variant in individuals. G439C is not present in gnomAD. G439C has not been functionally characterized. This residue is located in a Non_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 G439C around 11% (1/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-1.834 0.235 -1 0.588 6
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.

G439C 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
439 0
438 4 E438K, E438X,
440 4 P440L,
437 5
441 5 P441R, P441L,
436 7 T436M,
442 7
435 8 E435G, E435X,
443 8 T443N, T443fsX,
434 8
444 8 E444K, E444D, E444D,
433 9
445 9
432 10
446 10
431 11 F431L, F431L, F431L,
447 11 Y447X,
430 11
448 11 A448S, A448T,
429 12 A429P, A429V,
449 12
428 13 S428fsX, S428L, S428X,
450 13
427 13 Y427C, Y427H, Y427S,
451 13 P451L,
426 14 P426H,
452 14
425 14
453 14
424 15
454 15