KCNQ1 Variant D446E Detail

We estimate the penetrance of LQTS for KCNQ1 D446E is 10%. This variant was found in a total of 21 carriers in 2 papers or gnomAD, 2 had LQTS. D446E is present in 1 alleles in gnomAD. D446E has not been functionally characterized. This residue is located in a Non_Hotspot region for LQT1. In silico predictions, functional data (if available), and location in structure are equivalent to observing 1 individuals with LQT1 and 9 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 D446E around 10% (3/31).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-0.82 0.028 1 0.595 5
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 LQT1 Other Disease
29197658 2018 2 None 2 None
19716085 2009 2 None 2 None
LITERATURE, COHORT, AND GNOMAD: - 21 19 2
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.

D446E 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. This results from the fact that the functional KV7.1 channel 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
446 0 D446E, D446E, D446E, D446E, D446N,
445 4
447 4 P447H,
444 5 T444M, T444K,
448 5 P448R, P448Q, P448L, P448S,
443 7
449 7 E449K,
442 8 H442R,
450 8 E450K,
441 8 P441S,
451 8 R451Q, R451W,
440 9
452 9 R452Q, R452W, R452L,
439 10
453 10
438 11
454 11
437 11 M437V,
455 11 H455Y, H455Q, H455Q, H455R,
436 12
456 12 F456L, F456L, F456L,
435 13
457 13
434 13 G434R, G434R,
458 13
433 14 P433A,
459 14 D459N, D459V,
432 14 T432I, T432A,
460 14 G460S, G460D, G460C,
431 15 V431L, V431L,
461 15