KCNH2 Variant N598Q Detail

We estimate the penetrance of LQTS for KCNH2 N598Q is 70%. We are unaware of any observations of this variant in individuals. N598Q is not present in gnomAD. N598Q has been functionally characterized in 2 papers. 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 N598Q around 70% (6/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
None None None None 76
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.

Functional Data Homozygously Collected

Steady state (S.S.) and peak tail current are relative % to wildtype (100% being no different from wildtype). V0.5 act/inact are the voltages at which half of the maximal current is reached during an activation and inactivation protocol, each is 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 S.S Peak (%WT) Peak Tail IKr (%WT) V1/2 Act. V1/2 Inact. Recov. Inact. Deactivation (%WT)
9925876 HEK293 0 None None None None
12063277 HEK293 73 -2.2 None None None

Functional Data Heterozygously Collected

Functional parameters are the same as defined above.

PubMed ID Cell Type S.S Peak (%WT) Peak Tail IKr (%WT) V1/2 Act. V1/2 Inact. Deactivation (%WT)
9925876 HEK293 None None None
12063277 HEK293 None None None

N598Q 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
598 0
597 4 Y597C, Y597H,
599 4 S599N,
596 5 P596T, P596R, P596L, P596S,
600 5
595 7 K595N, K595N, K595E,
601 7 G601S,
594 8
602 8 L602X,
593 8 I593K, I593X, I593V, I593R, I593T,
603 8 G603D,
592 9 Q592X,
604 9 G604D, G604S, G604C,
591 10 D591H, D591N,
605 10 P605L,
590 11 G590D, G590V,
606 11 S606F, S606Del, S606P,
589 11 L589P,
607 11
588 12 N588K, N588D, N588K,
608 12
587 13
609 13 D609N, D609G,
586 13 L586M,
610 13
585 14 W585C, W585C,
611 14 Y611D,
584 14 G584C, G584S, G584R,
612 14 V612A, V612L, V612L,
583 15 I583V,
613 15 T613L, T613M, T613A, T613K,