We estimate the penetrance of LQTS for KCNH2 C39X is %.
This variant was found in a total of 3 carriers in 2 papers or gnomAD,
3 had LQTS.
C39X is not present in gnomAD.
C39X has been functionally characterized in 1 papers.
This residue is located in a None region for LQT2.
In Silico Data
Penetrance Density (%)
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).
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).