SCN5A Variant L173M

Summary of observed carriers, functional annotations, and structural context for SCN5A L173M. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

3%

0/10 effective observations

Estimated BrS1 penetrance

27%

2/10 effective observations

Total carriers

0

0 BrS1 · 0 LQT3 · 0 unaffected

L173M 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 0.577 37 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 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 L173M.
Neighbour residue Distance (Å) Observed variants
121 11 R121W, R121Q,
198 10
124 9 A124D,
114 12
170 6 F170I,
184 13 H184R,
171 7
137 13 I137V,
197 13
113 15 V113I, V113A,
129 15
169 7
177 5 L177P,
189 15
123 12 A123G, A123V,
127 11
125 11 V125L, V125L,
174 5 V174I,
133 12
182 14 C182R, C182Y,
134 15 N134S,
205 13 c.612-2A>G, Y205X
166 11 A166T,
179 11 R179X, R179Q,
172 5
185 12 A185T, A185V,
165 13
180 10 G180V,
120 11
126 15 K126E,
168 11
175 7 K175N, K175N,
202 13 I202T,
194 14
188 11
167 11
178 9 A178G,
128 10 c.381dupT,
201 12
118 14
181 11
176 6
173 0