SCN5A Variant F1317C

Summary of observed carriers, functional annotations, and structural context for SCN5A F1317C. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

5%

0/12 effective observations

Estimated BrS1 penetrance

13%

1/12 effective observations

Total carriers

2

0 BrS1 · 0 LQT3 · 2 unaffected

F1317C is present in 2 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 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 (%)
-7.08 1 -3.43 0.938 10 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 – 2 2 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 F1317C.
Neighbour residue Distance (Å) Observed variants
1659 7
1271 14 W1271C, W1271C,
1480 14 c.4437+5G>A, c.4438-1C>T,
1653 15
1315 7
1216 14 L1216V,
1314 6 c.3940_3941delCT,
1320 6 M1320I, M1320I, M1320I,
1666 13
1656 10
1313 7
1660 11 I1660V, I1660S,
1654 14
1310 12
1316 7 R1316Q, R1316L,
1319 5 G1319V,
1665 14
1663 11
1657 13
1662 8
1324 10
1317 0 F1317C,
1327 15
1318 5
1321 7 R1321K,
1323 10 V1323G,
1212 12 p.I1212del,
1322 10 c.3963+2T>C, c.3963+4A>G,
1312 10
1326 15 A1326S,
1311 12 L1311P,
1661 11 G1661R, G1661R, G1661E
1209 13 T1209R,
1655 10
1325 13 N1325S,
1208 14 E1208K, E1208X,
1664 15
1658 11