SCN5A Variant V1098L Detail

We estimate the penetrance of LQTS for SCN5A V1098L around 5% and the Brugada syndrome penetrance around 2%. SCN5A V1098L was found in a total of 40 carriers in 4 papers and/or in gnomAD: 0 had Brugada syndrome, 2 had LQTS. V1098L is present in 37 alleles in gnomAD. V1098L has been functionally characterized in 4 papers. This residue is located in a Non_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 (1 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 V1098L around 5% (2/50) and the Brugada syndrome penetrance around 2% (1/50).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density BrS (%) Penetrance Density LQT3 (%)
0.35 0.021 1.31 0.387 8 3
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
20541041 2010 2 2 0 0
27707468 2016 1 0 0 1 SUNDS
24529773 2014 1 0 0 1 SUNDS
20129283 2010 1 0 0 0
LITERATURE, COHORT, AND GNOMAD: - 40 38 2 0 -
VARIANT FEATURES ALONE: - 15 14 0 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.

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.
PubMed ID Year Cell Type Peak Current (%WT) V1/2 Act. (mV) V1/2 Inact. (mV) Late/Persistent Current (%WT)
20541041 2010
27707468 2016
24529773 2014
20129283 2010

V1098L 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. 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
1083 15 S1083C,
1084 14 G1084S, G1084R, G1084D,
1085 14
1086 13
1087 13
1088 12 A1088V, A1088T,
1089 11
1090 11 P1090Q, P1090L,
1091 10 D1091Y, D1091A,
1092 9
1093 8
1094 8
1095 7 W1095C, W1095X,
1096 5 S1096C, S1096G,
1097 4 Q1097H, c.3288+2delT,
1098 0 V1098L, V1098M,
1099 4
1100 5 A1100T, A1100V,
1101 7
1102 8 A1102T,
1103 8 S1103Y, S1103F,
1104 9
1105 10 E1105X, E1105V,
1106 11 A1106T,
1107 11 p.E1107RfsX24, E1107K, E1107X,
1108 12
1109 13 S1109G,
1110 13
1111 14
1112 14 Q1112X,
1113 15 A1113T, A1113V,