SCN5A Variant I120N

Summary of observed carriers, functional annotations, and structural context for SCN5A I120N. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

5%

0/10 effective observations

Estimated BrS1 penetrance

28%

2/10 effective observations

Total carriers

0

0 BrS1 · 0 LQT3 · 0 unaffected

I120N 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 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 (%)
NA NA NA 0.665 38 3

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 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 I120N.
Neighbour residue Distance (Å) Observed variants
126 10 K126E,
175 15 K175N, K175N,
113 15 V113I, V113A,
129 15
178 10 A178G,
128 13 c.381dupT,
117 11
119 4 P119S, P119L,
179 13 R179X, R179Q,
177 8 L177P,
123 6 A123G, A123V,
121 6 R121W, R121Q,
127 11
124 7 A124D,
118 6
125 9 V125L, V125L,
181 15
176 13
174 11 V174I,
115 10 S115G,
173 11
114 11
170 13 F170I,
116 11
180 13 G180V
120 0
122 7