KCNQ1 Variant R670K Detail

We estimate the penetrance of LQTS for KCNQ1 R670K is 5%. This variant was found in a total of 7 carriers in 3 papers or gnomAD, 0 had LQTS. R670K is present in 4 alleles in gnomAD. R670K has not been functionally characterized. This residue is located in a Non_Hotspot region for LQT1. In silico predictions, functional data (if available), and location in structure are equivalent to observing 0 individuals with LQT1 and 10 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 R670K around 5% (0/17).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
0.09 0.0 2 0.82 0
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
32164657 2020 1 1 None AF
25786344 2015 1 1 None None
24144883 2014 1 1 None Early onset AF
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.

R670K has 21 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
670 0 R670K,
669 4 R669S, R669S, R669T,
671 4 G671S,
668 5
672 5
667 7 V667M,
673 7 D673N,
666 8
674 8 E674K,
665 8
675 8
664 9
663 10 E663K,
662 11
661 11
660 12 P660S,
659 13
658 13 T658N,
657 14 N657S,
656 14
655 15