SCN5A Variant P656L Detail

We estimate the penetrance of LQTS for SCN5A P656L around 0% and the Brugada syndrome penetrance around 1%. SCN5A P656L was found in a total of 124 carriers in 1 papers and/or in gnomAD: 0 had Brugada syndrome, 0 had LQTS. P656L is present in 123 alleles in gnomAD. P656L has been functionally characterized in 1 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 P656L around 0% (0/134) and the Brugada syndrome penetrance around 1% (1/134).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density BrS (%) Penetrance Density LQT3 (%)
-6.89 0.975 -1.83 0.653 3 2
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
20129283 2010 1 0 0 0
LITERATURE, COHORT, AND GNOMAD: - 124 124 0 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)
20129283 2010

P656L 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
641 15
642 14
643 14
644 13
645 13
646 12 p.Q646RfsX5, c.1936delC,
647 11 A647S, A647V, A647D,
648 11 P648L,
649 10 C649R, C649Y,
650 9
651 8 c.1950_1953delAGAT, D651H,
652 8 G652S, G652D,
653 7
654 5 E654Q, E654X , E654K, E654D,
655 4 E655K,
656 0 P656L,
657 4
658 5 A658V,
659 7 R659Q, R659W,
660 8
661 8 R661W, R661Q,
662 9 c.1983_1993dupGGCCCTCAGCG, A662S,
663 10
664 11 S664G,
665 11 A665T, A665S,
666 12
667 13
668 13 V668I,
669 14
670 14
671 15 S671C,