KCNH2 Variant F340C Detail

We estimate the penetrance of LQTS for KCNH2 F340C is 10%. We are unaware of any observations of this variant in individuals. F340C is not present in gnomAD. F340C 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 F340C around 10% (1/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-5.427 0.999 -3 0.862 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.

F340C 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
340 0 F340L, F340L, F340L,
339 4
341 4
338 5
342 5 D342A, D342V, D342X,
337 7 T337S, T337S, T337X,
343 7 L343fsX,
336 8
344 8
335 8 Q335X,
345 8 G345S,
334 9 P334L,
346 9 D346Y, D346E, D346E, D346N,
333 10
347 10 P347S,
332 11
348 11
331 11 S331T, S331N,
349 11
330 12 I330V,
350 12
329 13
351 13 S351L,
328 13 R328fsX, R328H, R328C,
352 13
327 14 Y327H,
353 14 T353S, T353S,
326 14 R326C, R326fsX, R326H,
354 14
325 15 V325M,
355 15 D355G,