KCNQ1 Variant I443T Detail

We estimate the penetrance of LQTS for KCNQ1 I443T is 10%. We are unaware of any observations of this variant in individuals. I443T is not present in gnomAD. I443T 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 0 individuals with LQT1 and 10 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 I443T around 10% (0/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-0.87 0.73 -1 0.668 3
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
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.

I443T 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
443 0
442 4 H442R,
444 4 T444M, T444K,
441 5 P441S,
445 5
440 7
446 7 D446E, D446E, D446E, D446E, D446N,
439 8
447 8 P447H,
438 8
448 8 P448R, P448Q, P448L, P448S,
437 9 M437V,
449 9 E449K,
436 10
450 10 E450K,
435 11
451 11 R451Q, R451W,
434 11 G434R, G434R,
452 11 R452Q, R452W, R452L,
433 12 P433A,
453 12
432 13 T432I, T432A,
454 13
431 13 V431L, V431L,
455 13 H455Y, H455Q, H455Q, H455R,
430 14
456 14 F456L, F456L, F456L,
429 14 N429S,
457 14
428 15 D428G,
458 15