KCNQ1 Variant R555H Detail

We estimate the penetrance of LQTS for KCNQ1 R555H is 50%. This variant was found in a total of 14 carriers in 11 papers or gnomAD, 9 had LQTS. R555H is present in 4 alleles in gnomAD. R555H has been functionally characterized in 2 papers. 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 R555H around 50% (11/24).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-4.38 1.0 -1 0.924 39
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 6 None 6 None
30758498 2019 1 None None None
26412604 2016 1 None 1 None
25344363 2014 None None None None
24667783 2015 1 None 1 None
23631430 2013 1 None None None
22949429 2012 2 None 2 None
19841300 2009 2 None 2 None
19716085 2009 1 None 1 None
17192539 2006 1 None 1 None
14998624 2004 1 None 1 None
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.

Functional Data Homozygously Collected

Peak current is relative to wildtype (100% being no different from wildtype). V0.5 activation is the voltages at which half of the maximal current is reached during an activation in units of mV and relative to wildtype. Recovery from inactivation (Rec. inact.) and deactivation time (Deactivation) are the ratio of characteristic time constants with wildtype (unitless).

PubMed ID Cell Type Peak Current IKs (%WT) V1/2 Act. Activation time (%WT) Deactivation time (%WT)
25344363 CHO 12 50.0 1.089285714 0.717741935
25037568 CHO 35 49.8 1.406593407 0.6814814810000001

Functional Data Heterozygously Collected

Functional parameters are the same as defined above.

PubMed ID Cell Type Peak Current IKs (%WT) V1/2 Act. Activation time (%WT) Deactivation time (%WT)
25344363 CHO 12 40.0 1.089285714 1.451612903
25037568 CHO None None None

R555H has 15 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
555 7 R555H, R555C, R555S, R555L,
556 8
552 9 L552F,
554 9
553 9
559 10 L559P,
557 10 K557E,
558 10
560 11
551 11
549 12
550 12
548 13 G548S,
563 14
561 15