KCNH2 Variant L523P Detail

We estimate the penetrance of LQTS for KCNH2 L523P is 18%. We are unaware of any observations of this variant in individuals. L523P is not present in gnomAD. L523P 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 L523P around 18% (1/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-6.709 1.0 -3 0.919 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.

L523P has 34 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
523 0
522 4 G522E,
524 5
526 6
521 6
525 7 K525N, K525N,
429 7 A429P, A429V,
520 8
527 9
430 9
425 10
428 10 S428fsX, S428X, S428L,
426 10 P426H,
528 11 R528X, R528W, R528P,
508 11
432 11
529 12
574 12 M574L, M574L, M574V,
570 13
510 13
431 13 F431L, F431L, F431L,
566 13 C566S, C566G, C566R, C566F, C566S,
567 13 I567T, I567M,
530 14
503 14
506 14 I506V,
507 14 P507S, P507L,
427 14 Y427H, Y427S, Y427C,
509 15 D509N,
573 15
504 15 A504V,
563 15 W563X, W563C, W563G, W563C,
569 15 Y569C, Y569X, Y569H,
421 15 T421fsX, T421M,