KCNQ1 Variant R451W Detail

We estimate the penetrance of LQTS for KCNQ1 R451W is 32%. This variant was found in a total of 1 carriers in 2 papers or gnomAD, 1 had LQTS. R451W is not present in gnomAD. R451W has not been functionally characterized. This residue is located in a Mild_Hotspot region for LQT1. In silico predictions, functional data (if available), and location in structure are equivalent to observing 2 individuals with LQT1 and 8 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 R451W around 32% (3/11).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-3.63 1.0 -5 0.672 29
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
32893267 2020 1 None 1 None
19716085 2009 1 None 1 None
LITERATURE, COHORT, AND GNOMAD: - 1 0 1
VARIANT FEATURES ALONE: - 10 8 2 -
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.

R451W 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
451 0 R451Q, R451W,
450 4 E450K,
452 4 R452Q, R452W, R452L,
449 5 E449K,
453 5
448 7 P448R, P448Q, P448L, P448S,
454 7
447 8 P447H,
455 8 H455Y, H455Q, H455Q, H455R,
446 8 D446E, D446E, D446E, D446E, D446N,
456 8 F456L, F456L, F456L,
445 9
457 9
444 10 T444M, T444K,
458 10
443 11
459 11 D459N, D459V,
442 11 H442R,
460 11 G460S, G460D, G460C,
441 12 P441S,
461 12
440 13
462 13
439 13
463 13 S463T,
438 14
464 14 S464P,
437 14 M437V,
465 14
436 15
466 15