KCNH2 Variant L524R Detail

We estimate the penetrance of LQTS for KCNH2 L524R is 16%. We are unaware of any observations of this variant in individuals. L524R is not present in gnomAD. L524R 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 L524R around 16% (1/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-5.751 1.0 -2 0.979 16
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
LITERATURE, COHORT, AND GNOMAD: - 0 0 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.

L524R has 30 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
524 0
523 5
522 5 G522E,
525 5 K525N, K525N,
521 6
526 6
508 7
527 7
528 9 R528W, R528P, R528X,
506 9 I506V,
520 10
507 10 P507S, P507L,
510 10
503 10
429 10 A429V, A429P,
425 11
504 11 A504V,
509 11 D509N,
529 11
530 12
505 12 A505V,
428 12 S428fsX, S428X, S428L,
426 13 P426H,
531 13 R531Q, R531W, R531Del,
430 13
460 14 D460fsX,
502 14 M502I, M502I, M502I,
432 14
456 14 D456Y,
421 14 T421M, T421fsX,