SCN5A Variant Y162C

Summary of observed carriers, functional annotations, and structural context for SCN5A Y162C. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

5%

0/11 effective observations

Estimated BrS1 penetrance

24%

2/11 effective observations

Total carriers

1

0 BrS1 · 0 LQT3 · 1 unaffected

Y162C is present in 1 alleles 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 (%)
-7.74 0.999 -2.72 0.967 27 1

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 – 1 1 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 Y162C.
Neighbour residue Distance (Å) Observed variants
203 15
208 6 E208K,
205 10 Y205X, c.612-2A>G,
156 12 W156R, W156X,
168 11
158 6 K158T,
202 15 I202T,
206 12
163 6 c.486delC,
166 8 A166T,
167 11
161 5 E161K, E161Q,
201 13
219 13 p.R219HfsX11, R219C, R219H, c.656_657insATTCA,
169 11
144 13
151 14
222 12 R222X, R222Q, R222L,
218 14
159 7 Y159C, Y159X,
155 14
147 12
207 9
212 14 L212Q, L212P,
164 8 F164L
209 11 N209T, N209S,
157 9 T157I,
148 15
160 7 p.V160fs,
165 6
140 14
204 10 c.611+3_611+4dupAA, A204T, A204V, c.611+1G>A,
210 11 I210T,
162 0 Y162C, Y162H,