SCN5A Variant P116S

Summary of observed carriers, functional annotations, and structural context for SCN5A P116S. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

35%

1/10 effective observations

Estimated BrS1 penetrance

14%

1/10 effective observations

Total carriers

0 BrS1 · 0 LQT3 · 0 unaffected

P116S has not been reported in gnomAD. This residue resides in a Mild_Hotspot region for Brugada syndrome and a Hotspot region for LQT3.

Variant features alone are equivalent to phenotyping 1 individuals for Brugada syndrome and 1 individuals for LQT3.

In silico predictors

Variant-level computational predictors.
PROVEAN	PolyPhen-2	BLAST-PSSM	REVEL	Penetrance Density BrS (%)	Penetrance Density LQT3 (%)
NA	NA	NA	0.91	11	45

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	–	0	0	0	0		–
Variant features alone	–	15	13	1	1	–	–

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 P116S.
Neighbour residue	Distance (Å)	Observed variants
126	12	K126E,
113	9	V113I, V113A,
178	10	A178G,
117	4
119	9	P119S, P119L,
179	10	R179X, R179Q,
177	11	L177P,
123	12	A123G, A123V,
121	6	R121W, R121Q,
124	12	A124D,
118	6
125	10	V125L, V125L,
181	13
176	14
174	15	V174I,
115	4	S115G,
182	15	C182R, C182Y,
112	6	Y112C,
114	7
184	12	H184R
116	0
180	10	G180V,
120	11
183	14
122	6