KCNH2 Variant G601C Detail

We estimate the penetrance of LQTS for KCNH2 G601C is 69%. We are unaware of any observations of this variant in individuals. G601C is not present in gnomAD. G601C has not been functionally characterized. This residue is located in a Hotspot region for LQT2. In silico predictions, functional data (if available), and location in structure are equivalent to observing 6 individuals with LQT2 and 4 unaffected individuals.These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 G601C around 69% (6/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-2.34 0.996 -2 0.738 71
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 LQT2 Other Disease
LITERATURE, COHORT, AND GNOMAD: - 0 0 0 -
VARIANT FEATURES ALONE: - 10 4 6 -
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.

G601C 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 since the functional KV11.1 channel (protein product of KCNH2/hERG) 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
601 0 G601S,
600 4
602 4 L602X,
599 5 S599N,
603 5 G603D,
598 7
604 7 G604S, G604D, G604C,
597 8 Y597H, Y597C,
605 8 P605L,
596 8 P596L, P596S, P596T, P596R,
606 8 S606P, S606F, S606Del,
595 9 K595N, K595E, K595N,
607 9
594 10
608 10
593 11 I593X, I593V, I593R, I593K, I593T,
609 11 D609N, D609G,
592 11 Q592X,
610 11
591 12 D591N, D591H,
611 12 Y611D,
590 13 G590D, G590V,
612 13 V612L, V612A, V612L,
589 13 L589P,
613 13 T613A, T613L, T613K, T613M,
588 14 N588K, N588K, N588D,
614 14 A614T, A614V,
587 14
615 14 L615V, L615F,
586 15 L586M,
616 15 Y616S,