SCN5A Variant R481W Detail

We estimate the penetrance of LQTS for SCN5A R481W around 0% and the Brugada syndrome penetrance around 0%. SCN5A R481W was found in a total of 360 carriers in 3 papers and/or in gnomAD: 1 had Brugada syndrome, 1 had LQTS. R481W is present in 352 alleles in gnomAD. R481W has been functionally characterized in 7 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 R481W around 0% (1/370) and the Brugada syndrome penetrance around 0% (1/370).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density BrS (%) Penetrance Density LQT3 (%)
-4.62 0.009 0.47 None 2 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
23293604 2012 1 0 1 0
23714088 2013 1 1 0 0
20129283 2010 6 0 0 0
LITERATURE, COHORT, AND GNOMAD: - 360 358 1 1 -
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.

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)
15992732 2005 HEK 137 1 -6
15851227 2004
15898185 2004
23293604 2012
23714088 2013
15992733 2005
20129283 2010

R481W 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
466 15 L466F,
467 14
468 14 P468L,
469 13 V469I,
470 13 N470K,
471 12
472 11
473 11 E473X,
474 10 R474G, R474K,
475 9 R475K, R475S,
476 8
477 8 c.1428_1431delCAAG,
478 7
479 5
480 4 K480N,
481 0 R481W, R481Q,
482 4 M482I,
483 5
484 7
485 8
486 8 T486A, T486S,
487 9
488 10
489 11
490 11 G490A, G490E,
491 12 E491G,
492 13
493 13 R493K,
494 14
495 14
496 15 K496M, K496N,