KCNH2 Variant N339D Detail

We estimate the penetrance of LQTS for KCNH2 N339D is 7%. We are unaware of any observations of this variant in individuals. N339D is not present in gnomAD. N339D 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 0 individuals with LQT2 and 10 unaffected individuals.These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 N339D around 7% (0/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-3.39 0.972 1 0.685 2
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 10 0 -
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.

N339D 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
339 0
338 4
340 4 F340L, F340L, F340L,
337 5 T337S, T337S, T337X,
341 5
336 7
342 7 D342V, D342A, D342X,
335 8 Q335X,
343 8 L343fsX,
334 8 P334L,
344 8
333 9
345 9 G345S,
332 10
346 10 D346N, D346E, D346E, D346Y,
331 11 S331T, S331N,
347 11 P347S,
330 11 I330V,
348 11
329 12
349 12
328 13 R328H, R328C, R328fsX,
350 13
327 13 Y327H,
351 13 S351L,
326 14 R326H, R326fsX, R326C,
352 14
325 14 V325M,
353 14 T353S, T353S,
324 15 L324L,
354 15