KCNH2 Variant D355Y Detail

We estimate the penetrance of LQTS for KCNH2 D355Y is 10%. We are unaware of any observations of this variant in individuals. D355Y is not present in gnomAD. D355Y 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 D355Y around 10% (1/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-3.457 0.994 -3 0.75 1
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.

D355Y 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
355 0 D355G,
354 4
356 4 R356H, R356C,
353 5 T353S, T353S,
357 5 E357D, E357D,
352 7
358 7
351 8 S351L,
359 8 I359V,
350 8
360 8
349 9
361 9
348 10
362 10
347 11 P347S,
363 11 I363X,
346 11 D346Y, D346N, D346E, D346E,
364 11 K364X,
345 12 G345S,
365 12 E365G,
344 13
366 13 R366Q, R366X,
343 13 L343fsX,
367 13 T367S, T367S,
342 14 D342A, D342V, D342X,
368 14 H368Y,
341 14
369 14 N369K, N369K,
340 15 F340L, F340L, F340L,
370 15