KCNH2 Variant L452V Detail

We estimate the penetrance of LQTS for KCNH2 L452V is 46%. We are unaware of any observations of this variant in individuals. L452V is not present in gnomAD. L452V has not been functionally characterized. This residue is located in a Hotspot region for LQT2. In silico predictions, functional data (if available), and location in structure are equivalent to observing 4 individuals with LQT2 and 6 unaffected individuals.These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 L452V around 46% (4/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-2.722 0.978 1 0.759 57
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.

L452V has 29 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
452 0
453 4
451 5 P451L,
450 6
455 6
456 7 D456Y,
454 7
424 8
420 9 Y420C,
428 9 S428X, S428L, S428fsX,
449 10
427 10 Y427H, Y427S, Y427C,
457 10 L457P,
458 11
425 11
459 11
423 12
432 12
421 12 T421M, T421fsX,
460 12 D460fsX,
525 13 K525N, K525N,
426 13 P426H,
429 13 A429P, A429V,
528 13 R528X, R528W, R528P,
431 14 F431L, F431L, F431L,
422 14 A422T,
417 14
430 15
607 15