SCN5A Variant P566A Detail

We estimate the penetrance of LQTS for SCN5A P566A around 6% and the Brugada syndrome penetrance around 16%. SCN5A P566A was found in a total of 0 carriers in 0 papers and/or in gnomAD: 0 had Brugada syndrome, 0 had LQTS. P566A is not present in gnomAD. P566A has been functionally characterized in 0 papers. This residue is located in a Mild_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 P566A around 6% (0/10) and the Brugada syndrome penetrance around 16% (1/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density BrS (%) Penetrance Density LQT3 (%)
NA NA NA 0.298 19 6
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 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.

P566A 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
551 15 A551T, A551V,
552 14 G552R, G552W,
553 14 E553K, E553X,
554 13 S554N, S554I,
555 13 E555K,
556 12
557 11 H557Y, H557Q, H557L,
558 11 H558R,
559 10 T559R, T559I,
560 9
561 8
562 8
563 7 V563G,
564 5
565 4
566 0
567 4 L567Q,
568 5 R568H, R568C,
569 7 c.1705dupC, R569W, R569Q,
570 8 T570N,
571 8 S571I,
572 9 A572D, A572V, A572F, A572S,
573 10 Q573E, Q573R, Q573X,
574 11 c.1721delG, G574E,
575 11
576 12
577 13 S577N,
578 13 P578T, P578R,
579 14 G579R,
580 14
581 15 S581L,