KCNH2 Variant A350G Detail

We estimate the penetrance of LQTS for KCNH2 A350G is 8%. We are unaware of any observations of this variant in individuals. A350G is not present in gnomAD. A350G 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 A350G around 8% (0/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-1.722 0.76 0 0.575 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 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.

A350G 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
350 0
349 4
351 4 S351L,
348 5
352 5
347 7 P347S,
353 7 T353S, T353S,
346 8 D346E, D346Y, D346E, D346N,
354 8
345 8 G345S,
355 8 D355G,
344 9
356 9 R356C, R356H,
343 10 L343fsX,
357 10 E357D, E357D,
342 11 D342A, D342V, D342X,
358 11
341 11
359 11 I359V,
340 12 F340L, F340L, F340L,
360 12
339 13
361 13
338 13
362 13
337 14 T337S, T337X, T337S,
363 14 I363X,
336 14
364 14 K364X,
335 15 Q335X,
365 15 E365G,