KCNQ1 Variant F456V Detail

We estimate the penetrance of LQTS for KCNQ1 F456V is 12%. We are unaware of any observations of this variant in individuals. F456V is not present in gnomAD. F456V 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 F456V around 12% (1/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-1.29 0.016 -1 0.659 8
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
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.

F456V 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
456 0 F456L, F456L, F456L,
455 4 H455Y, H455Q, H455Q, H455R,
457 4
454 5
458 5
453 7
459 7 D459N, D459V,
452 8 R452Q, R452W, R452L,
460 8 G460S, G460D, G460C,
451 8 R451Q, R451W,
461 8
450 9 E450K,
462 9
449 10 E449K,
463 10 S463T,
448 11 P448R, P448Q, P448L, P448S,
464 11 S464P,
447 11 P447H,
465 11
446 12 D446E, D446E, D446E, D446E, D446N,
466 12
445 13
467 13 K467R,
444 13 T444M, T444K,
468 13 S468G, S468N,
443 14
469 14
442 14 H442R,
470 14
441 15 P441S,
471 15