We estimate the penetrance of LQTS for SCN5A Y774D around
21% and the Brugada syndrome penetrance around
26%. SCN5A Y774D was found in a total of
1 carriers in 0 papers and/or in gnomAD:
0 had Brugada syndrome, 0 had LQTS.
Y774D is present in 1 alleles in gnomAD.
Y774D has been functionally characterized in 0 papers.
This residue is located in a Mild_Hotspot region for Brugada syndrome and a Mild_Hotspot
region for LQTS.
In silico predictions, functional data (if available), and location in structure are equivalent to phenotyping
10 individuals for Brugada syndrome (2 diagnosed with Brugada syndrome) and 5 individuals for LQTS (1
with LQTS). These data combined with observations of carriers lead us to estimate the LQTS penetrance for SCN5A
Y774D around 21% (1/11)
and the Brugada syndrome penetrance around 26%
(2/11).
In Silico Data
PROVEAN
PolyPhen-2
BLAST-PSSM
REVEL
Penetrance Density BrS (%)
Penetrance Density LQT3 (%)
-9.73
0.979
-2.71
0.919
32
23
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).
Reported Carrier Data
PubMed ID
Year
Carriers
Unaffected
LQT3
BrS1
Other
Other Disease
LITERATURE, COHORT, AND GNOMAD:
-
1
1
0
0
-
VARIANT FEATURES ALONE:
-
15
12
1
2
-
-
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.
Y774D has 16 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.