SCN5A Variant N109T

Summary of observed carriers, functional annotations, and structural context for SCN5A N109T. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

18%

0/10 effective observations

Estimated BrS1 penetrance

34%

3/10 effective observations

Total carriers

0

0 BrS1 · 0 LQT3 · 0 unaffected

N109T has not been reported in gnomAD. This residue resides in a Non_Hotspot region for Brugada syndrome and a Mild_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 0.489 49 23

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 N109T.
Neighbour residue Distance (Å) Observed variants
94 15 I94V, I94S,
95 14 V95I, V95L, V95L,
96 14
97 13
98 13
99 12
100 11
101 11 T101I,
102 10
103 9
104 8 R104G, R104W, R104Q,
105 8
106 7 S106T,
107 5
108 4
109 0 N109K, N109K,
110 4 A110T,
111 5
112 7 Y112C,
113 8 V113I, V113A,
114 8
115 9 S115G,
116 10
117 11
118 11
119 12 P119S, P119L,
120 13
121 13 R121W, R121Q,
122 14
123 14 A123G, A123V,
124 15 A124D