SCN5A Variant T169I

Summary of observed carriers, functional annotations, and structural context for SCN5A T169I. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

4%

0/10 effective observations

Estimated BrS1 penetrance

17%

1/10 effective observations

Total carriers

0

0 BrS1 · 0 LQT3 · 0 unaffected

T169I has not been reported 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 1 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 0.944 16 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 14 0 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 T169I.
Neighbour residue Distance (Å) Observed variants
198 9
124 14 A124D,
164 10 F164L, F164L, F164L,
209 14 N209S, N209T,
170 6 F170I,
171 7
137 11 I137V,
197 11
163 10 c.486delC,
196 15
169 0
177 12 L177P,
222 14 R222X, R222Q, R222L,
127 15
174 9 V174I,
133 13
160 14 p.V160fs,
205 8 c.612-2A>G, Y205X,
206 13
166 5 A166T,
144 15
172 5
199 12 S199T,
165 6
204 10 A204T, c.611+1G>A, c.611+3_611+4dupAA, A204V,
162 11 Y162H, Y162C,
203 13
208 11 E208K,
136 14 L136P,
168 6
175 10 K175N, K175N,
202 10 I202T,
194 14
141 14 I141V, I141N,
188 14
167 6
178 15 A178G,
128 14 c.381dupT,
161 13 E161K, E161Q,
201 7
225 12 R225W, R225Q
176 11
207 14
173 7
200 11
140 12