KCNQ1 Variant A384S Detail

We estimate the penetrance of LQTS for KCNQ1 A384S is 43%. We are unaware of any observations of this variant in individuals. A384S is not present in gnomAD. A384S 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 4 individuals with LQT1 and 6 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 A384S around 43% (4/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-2.35 0.552 1 0.579 50
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 6 4 -
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.

A384S has 35 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
384 0
383 4
385 4 E385K,
515 6
381 6 C381Y,
392 6 W392R, W392R, W392ins,
518 6 R518Q, R518G,
386 6 N386K, N386K,
387 7 P387T,
382 7
391 7 T391A, T391I,
389 8 S389P,
514 8 I514T,
379 9 W379R, W379R, W379C, W379C, W379G,
380 9 R380S, R380S, R380G,
511 9 R511Q, R511W,
512 9
519 10 R519H, R519C,
378 10 A378T,
388 10 D388H, D388N,
516 10
390 11
377 11
517 11 I517T,
513 11 T513A, T513S, T513S,
510 12 H510R, H510Y,
522 12 Y522S,
508 12 E508G,
521 12
393 13 K393N,
520 14 M520R,
376 14
394 14 I394L,
523 14
509 15 H509Q, H509Q, H509R,