SCN5A Variant N592K Detail

We estimate the penetrance of LQTS for SCN5A N592K around 0% and the Brugada syndrome penetrance around 13%. SCN5A N592K was found in a total of 11 carriers in 3 papers and/or in gnomAD: 1 had Brugada syndrome, 0 had LQTS. N592K is present in 8 alleles in gnomAD. N592K has been functionally characterized in 3 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 N592K around 0% (0/21) and the Brugada syndrome penetrance around 13% (2/21).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density BrS (%) Penetrance Density LQT3 (%)
-2.54 0.684 -0.28 0.821 4 0
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
24463578 2014 2 0 1 0
26154754 2015 1 0 1 0
20129283 2010 1 0 0 0
LITERATURE, COHORT, AND GNOMAD: - 11 10 0 1 -
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)
24463578 2014 HEK 17 3.2 1.2
26154754 2015
20129283 2010

N592K 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
577 15 S577N,
578 14 P578T, P578R,
579 14 G579R,
580 13
581 13 S581L,
582 12
583 11 P583L,
584 11 G584R,
585 10
586 9 A586G, p.586_587delAL, A586T,
587 8
588 8 H588R, H588N,
589 7
590 5 K590Q,
591 4
592 0 N592S, N592K,
593 4
594 5
595 7
596 8 D596G,
597 8 C597G, C597Y,
598 9
599 10 G599R,
600 11
601 11 V601A,
602 12
603 13
604 13 L604V,
605 14 G605E,
606 14 A606T,
607 15 G607D, G607R, G607V,