SCN5A Variant I783T

Summary of observed carriers, functional annotations, and structural context for SCN5A I783T. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT3 penetrance

2%

0/11 effective observations

Estimated BrS1 penetrance

20%

2/11 effective observations

Total carriers

1

0 BrS1 · 0 LQT3 · 1 unaffected

I783T 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 (%)
-4.84 0.491 -1.64 0.914 25 2

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 I783T.
Neighbour residue Distance (Å) Observed variants
773 11 P773S,
760 15 p.F760SfsX5,
780 4
776 7 p.Y776del,
765 14
792 15
764 10 M764K, M764R,
777 5 F777L,
791 12 L791F,
819 15
781 8 W781X,
788 10 I788V,
782 5 N782T,
820 13
774 13 Y774D, Y774C, c.2320delT, p.Y774TfsX28,
767 12
775 13
814 14 R814Q,
816 14 F816L, F816Y,
813 12 c.2437-5C>A, c.2436+12G>A,
768 11
786 6
817 12 K817E,
761 15
779 7 Q779K, Q779X,
778 9
790 10
784 6 F784L,
772 14 D772N,
771 13 L771V,
785 7 D785N,
783 0 I783T,
789 11 V789I, V789A,
787 6