KCNQ1 Variant P448Q Detail

We estimate the penetrance of LQTS for KCNQ1 P448Q is 5%. This variant was found in a total of 18 carriers in 0 papers or gnomAD, 0 had LQTS. P448Q is present in 18 alleles in gnomAD. P448Q 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 P448Q around 5% (1/28).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-0.77 0.001 -1 0.512 4
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.

P448Q 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
448 0 P448R, P448Q, P448L, P448S,
447 4 P447H,
449 4 E449K,
446 5 D446E, D446E, D446E, D446E, D446N,
450 5 E450K,
445 7
451 7 R451Q, R451W,
444 8 T444M, T444K,
452 8 R452Q, R452W, R452L,
443 8
453 8
442 9 H442R,
454 9
441 10 P441S,
455 10 H455Y, H455Q, H455Q, H455R,
440 11
456 11 F456L, F456L, F456L,
439 11
457 11
438 12
458 12
437 13 M437V,
459 13 D459N, D459V,
436 13
460 13 G460S, G460D, G460C,
435 14
461 14
434 14 G434R, G434R,
462 14
433 15 P433A,
463 15 S463T,