KCNQ1 Variant K515M Detail

We estimate the penetrance of LQTS for KCNQ1 K515M is 39%. We are unaware of any observations of this variant in individuals. K515M is not present in gnomAD. K515M has not been functionally characterized. This residue is located in a Hotspot region for LQT1. In silico predictions, functional data (if available), and location in structure are equivalent to observing 3 individuals with LQT1 and 7 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 K515M around 39% (3/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-3.61 0.997 -2 0.748 41
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 7 3 -
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.

K515M 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
515 0
516 5
512 5
384 6
518 6 R518Q, R518G,
519 6 R519H, R519C,
514 6 I514T,
381 7 C381Y,
385 7 E385K,
513 7 T513A, T513S, T513S,
517 8 I517T,
511 9 R511Q, R511W,
392 9 W392R, W392R, W392ins,
383 9
520 10 M520R,
510 10 H510R, H510Y,
380 10 R380S, R380S, R380G,
521 11
387 11 P387T,
508 11 E508G,
523 11
522 11 Y522S,
386 11 N386K, N386K,
382 11
509 12 H509Q, H509Q, H509R,
391 12 T391A, T391I,
378 12 A378T,
377 12
389 13 S389P,
379 13 W379R, W379R, W379C, W379C, W379G,
388 15 D388H, D388N,