We estimate the penetrance of LQTS for SCN5A D1690N around
3% and the Brugada syndrome penetrance around
52%. SCN5A D1690N was found in a total of
3 carriers in 3 papers and/or in gnomAD:
2 had Brugada syndrome, 0 had LQTS.
D1690N is present in 1 alleles in gnomAD.
D1690N has been functionally characterized in 5 papers.
This residue is located in a Hotspot region for Brugada syndrome and a Non_Hotspot
region for LQTS.
In silico predictions, functional data (if available), and location in structure are equivalent to phenotyping
10 individuals for Brugada syndrome (4 diagnosed with Brugada syndrome) and 5 individuals for LQTS (0
with LQTS). These data combined with observations of carriers lead us to estimate the LQTS penetrance for SCN5A
D1690N around 3% (0/13)
and the Brugada syndrome penetrance around 52%
(6/13).
In Silico Data
PROVEAN
PolyPhen-2
BLAST-PSSM
REVEL
Penetrance Density BrS (%)
Penetrance Density LQT3 (%)
-4.79
1
-0.31
0.838
72
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 BrS/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
Peak and late/persistent 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.
D1690N has 51 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. All variants shown in the rightmost
column have been observed in at least one individual in the literature or gnomAD.