We estimate the penetrance of LQTS for KCNH2 C39R is 4%.
This variant was found in a total of 27 carriers in 0 papers or gnomAD (version 4),
0 had LQTS.
C39R is present in 27 alleles in gnomAD.
We have tested the trafficking efficiency of this variant, 126% of WT
with a standard error of 14%; in our analysis we used SE < 20% as 'high quality'.
Approximately below 50% of WT is considered PS3 moderate and below 30% is PS3 strong.
C39R has not been functionally characterized.
This residue is located in a Mild_Hotspot region for LQT2.
In silico predictions, functional data (if available), and location in structure are equivalent to observing
1 individuals with LQT2 and 9 unaffected individuals.These data combined with observations of carriers
lead us to estimate the LQTS penetrance for KCNQ1 C39R around
4% (1/37).
In Silico Data
PROVEAN
PolyPhen-2
BLAST-PSSM
REVEL
Penetrance Density (%)
-6.998
0.999
-5
0.934
37
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:
-
27
6
0
-
VARIANT FEATURES ALONE:
-
10
9
1
-
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.
C39R has 50 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.