SCN5A Variant P1002S

Summary of observed carriers, functional annotations, and structural context for SCN5A P1002S. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

0%

0/16 effective observations

Estimated BrS1 penetrance

16%

2/16 effective observations

Total carriers

6

0 BrS1 · 0 LQT3 · 6 unaffected

P1002S is present in 6 alleles in gnomAD. This residue resides in a Mild_Hotspot region for Brugada syndrome and a Non_Hotspot region for LQT3.

Variant features alone are equivalent to phenotyping 2 individuals for Brugada syndrome and 0 individuals for LQT3.

In silico predictors

Variant-level computational predictors.
PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density BrS (%) Penetrance Density LQT3 (%)
-0.23 0.01 0.6 0.518 35 1

PROVEAN scores below -2 suggest deleterious impact. REVEL scores above 0.5–0.75 are often interpreted as likely pathogenic. PolyPhen-2 scores above 0.85 are typically pathogenic. Penetrance density summarises neighbouring residue risk (Kroncke et al. 2019).

Reported carrier data

Observed carriers by publication or cohort.
Source Year Carriers Unaffected LQT3 BrS1 Other Other Disease
Literature, cohort, and gnomAD – 6 6 0 0 –
Variant features alone – 15 13 0 2 – –

Totals may differ from individual publications due to duplicate patients removed during curation.

Nearby variants

Neighbouring residues within 15 Ångström provide structural context. Variants listed in the right-most column have been observed clinically or in gnomAD.

Previously observed variants near P1002S.
Neighbour residue Distance (Å) Observed variants
987 15
988 14 R988W, R988Q,
989 14
990 13
991 13 K991E, K991T,
992 12
993 11 A993T, A993S,
994 11 A994V, A994T,
995 10 L995F,
996 9 A996T,
997 8 A997S, A997T, A997D
998 8
999 7 G999D,
1000 5 Q1000X, p.Gln1000del, Q1000L,
1001 4
1002 0 c.3005-3012delCCAGCTGG, P1002S,
1003 4
1004 5 C1004R,
1005 7 I1005V, I1005T,
1006 8 A1006S,
1007 8 T1007I, T1007N,
1008 9 P1008S,
1009 10
1010 11
1011 11 P1011S, P1011L,
1012 12
1013 13
1014 13 P1014S,
1015 14 E1015K, p.G1015DfsX14,
1016 14 T1016M, c.3045_3046delGA,
1017 15