KCNQ1 Variant Q521H Detail

We estimate the penetrance of LQTS for KCNQ1 Q521H is 60%. We are unaware of any observations of this variant in individuals. Q521H is not present in gnomAD. Q521H 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 5 individuals with LQT1 and 5 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 Q521H around 60% (5/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-2.43 0.986 -1 0.786 69
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 5 5 -
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.

Q521H has 37 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
521 0
520 6 M520R,
517 6 I517T,
377 6
524 6 V524G,
518 7 R518Q, R518G,
380 7 R380S, R380S, R380G,
522 7 Y522S,
525 8 A525T, A525V,
523 8
519 8 R519H, R519C,
373 9 S373P,
381 9 C381Y,
516 9
376 9
378 10 A378T,
514 10 I514T,
374 10 L374H, L374F,
515 11
528 11
526 11 K526Q, K526E,
513 12 T513A, T513S, T513S,
527 12
372 12
375 12
384 12
370 12 A370V,
379 13 W379R, W379R, W379C, W379C, W379G,
383 13
391 13 T391A, T391I,
371 13 A371T,
512 14
392 14 W392R, W392R, W392ins,
394 14 I394L,
529 14
369 15
382 15