SCN5A Variant T163S

Summary of observed carriers, functional annotations, and structural context for SCN5A T163S. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

3%

0/10 effective observations

Estimated BrS1 penetrance

39%

3/10 effective observations

Total carriers

0

0 BrS1 · 0 LQT3 · 0 unaffected

T163S has not been reported in gnomAD. This residue resides in a Hotspot region for Brugada syndrome and a Non_Hotspot region for LQT3.

Variant features alone are equivalent to phenotyping 3 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 (%)
NA NA NA 0.674 57 0

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 12 0 3 – –

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 T163S.
Neighbour residue Distance (Å) Observed variants
147 11
164 5 F164L, F164L, F164L,
170 11 F170I,
171 13
143 11
137 12 I137V,
142 15
156 15 W156R, W156R, W156X,
158 10 K158T,
163 0 c.486delC,
169 10
222 13 R222X, R222Q, R222L,
157 10 T157I,
160 5 p.V160fs,
205 13 c.612-2A>G, Y205X,
166 5 A166T,
144 11
172 15
139 13 p.I137_C139dup,
148 14
165 6
204 12 A204T, c.611+1G>A, c.611+3_611+4dupAA, A204V,
162 6 Y162H, Y162C,
146 15 V146M, V146A,
208 11 E208K,
136 13 L136P,
168 9
141 13 I141V, I141N,
167 6
161 7 E161K, E161Q,
201 13
225 14 R225W, R225Q
151 15
159 7 Y159C, Y159X,
207 14
145 15
140 9