SCN5A Variant A665P Detail

We estimate the penetrance of LQTS for SCN5A A665P around 5% and the Brugada syndrome penetrance around 8%. SCN5A A665P was found in a total of 0 carriers in 0 papers and/or in gnomAD: 0 had Brugada syndrome, 0 had LQTS. A665P is not present in gnomAD. A665P has been functionally characterized in 0 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 (0 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 A665P around 5% (0/10) and the Brugada syndrome penetrance around 8% (0/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density BrS (%) Penetrance Density LQT3 (%)
NA NA NA 0.613 3 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
LITERATURE, COHORT, AND GNOMAD: - 0 0 0 0 -
VARIANT FEATURES ALONE: - 15 15 0 0 - -
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.

A665P 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
650 15
651 14 D651H, c.1950_1953delAGAT,
652 14 G652S, G652D,
653 13
654 13 E654D, E654K, E654Q, E654X ,
655 12 E655K,
656 11 P656L,
657 11
658 10 A658V,
659 9 R659Q, R659W,
660 8
661 8 R661W, R661Q,
662 7 A662S, c.1983_1993dupGGCCCTCAGCG,
663 5
664 4 S664G,
665 0 A665S, A665T,
666 4
667 5
668 7 V668I,
669 8
670 8
671 9 S671C,
672 10 A672T, A672S,
673 11 L673V, L673P,
674 11
675 12 c.2024_2025delAG,
676 13
677 13 E677V,
678 14
679 14
680 15 R680C, R680H,