SCN5A Variant L793F

Summary of observed carriers, functional annotations, and structural context for SCN5A L793F. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

4%

0/11 effective observations

Estimated BrS1 penetrance

8%

0/11 effective observations

Total carriers

1

0 BrS1 · 0 LQT3 · 1 unaffected

L793F 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 0 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 (%)
-3.96 0.939 -0.79 0.845 2 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 – 1 1 0 0 –
Variant features alone – 15 15 0 0 – –

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 L793F.
Neighbour residue Distance (Å) Observed variants
758 9 G758E,
811 11 R811H, c.2435_2436+3delTGGTAinsCGCCT, R811G,
808 13 R808C, R808P, R808H,
760 11 p.F760SfsX5,
765 12
759 12 p.I759FfsX6, c.2274delG, I759V,
792 4
764 12 M764K, M764R,
755 13
791 7 L791F,
806 15 V806M,
800 10 R800C, R800L, R800H,
754 10
797 7 G797V,
801 13 M801V, p.801_803delMSN/insS,
750 14 Q750R,
788 9 I788V,
798 10
793 0 L793F,
762 12
810 12
756 13
814 12 R814Q,
807 10
813 14 c.2437-5C>A, c.2436+12G>A,
757 7
786 10
761 8
752 14 G752R,
809 14
790 6
784 15 F784L,
763 15 E763D, E763K
796 6
785 13 D785N,
789 6 V789A, V789I,
753 12
795 7
799 11
787 11
794 6