SCN5A Variant S309C

Summary of observed carriers, functional annotations, and structural context for SCN5A S309C. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

3%

0/11 effective observations

Estimated BrS1 penetrance

11%

1/11 effective observations

Total carriers

1

0 BrS1 · 0 LQT3 · 1 unaffected

S309C is present in 1 alleles in gnomAD. This residue resides in a Non_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 (%)
-2.89 0.828 -1.97 0.536 9 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 – 1 1 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 S309C.
Neighbour residue Distance (Å) Observed variants
294 15 V294M,
295 14 E295K,
296 14
297 13
298 13 G298S, G298D,
299 12 L299F, L299M, L299F,
300 11 V300I,
301 11
302 10
303 9
304 8
305 8 D305N
306 7 L306F, L306V,
307 5
308 4
309 0 S309C, S309N,
310 4 D310N,
311 5
312 7 E312K, c.934+1G>A, c.934+4C>T,
313 8
314 8
315 9 L315P,
316 10
317 11 K317N, K317E, K317N, K317M,
318 11
319 12 G319S, G319C, G319R,
320 13 T320N,
321 13 S321Y,
322 14
323 14
324 15