KCNH2 Variant L799sp

Summary of observed carriers, functional annotations, and structural context for KCNH2 L799sp. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT2 penetrance

%

NA/NA effective observations

Total carriers

5

5 LQT2 · 0 unaffected

Functional studies

0

Publications with functional data

L799sp has not been reported in gnomAD. This residue resides in a None region for LQT2.

In silico predictors

Variant-level computational predictors.
PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density LQT2 (%)
None None None None

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. BLAST-PSSM reflects evolutionary conservation; more negative values indicate rarer substitutions. Penetrance density summarises neighbouring residue risk (Kroncke et al. 2019).

Reported carrier data

Observed carriers by publication or cohort.
Source Year Carriers Unaffected LQT2 Other Disease
11854117 2002 5 0 5
10973849 2000 1 0 1
15840476 2005 3 0 3
15840476 2005 1 0 1
Literature, cohort, and gnomAD – 5 0 5 –
Variant features alone – 10 NA NA –

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. Note that some residues appear multiple times at different distances since the functional KV11.1 channel (protein product of KCNH2/hERG) is a homotetramer and occasionally the same residue from multiple subunits is present within the 15Å window.

Previously observed variants near L799sp.
Neighbour residue Distance (Å) Observed variants
799 0 L799sp,
800 4
787 5
798 5 I798fsX,
803 5 D803Y, D803X,
797 6 A797T,
786 7
782 7 I782fsX, I782N,
859 7 T859M, T859R,
788 7 E788K, E788D, E788D,
789 7
805 7 F805S, F805C,
860 8
56 8 R56Q,
43 8 Y43D, Y43C,
785 8 G785S, G785fsX, G785D,
804 8
801 9 K801T,
42 9 I42N,
44 9 C44F, C44X, C44W,
60 9 M60T,
802 9
822 9 V822M, V822L, V822L,
796 10 V796L, V796L, V796Del,
824 10
828 10
825 10
783 10 S783P,
780 11
830 11
858 11 I858V, I858T,
781 11
795 11 V795I,
806 11 G806R, G806R,
790 11
826 11 T826A, T826I,
57 11 A57P,
16 12 D16A,
19 12 I19F,
15 12 L15V,
41 12 V41A,
823 12 R823W, R823fsX, R823T, R823Q,
31 12 I31S,
45 12 N45D, N45K, N45K,
61 12 Q61R,
769 12
862 12 L862P,
829 12 D829A, D829E, D829E,
46 13 D46Y, D46E, D46E,
763 13
59 13
784 13 R784G, R784W, R784Q,
820 13 G820R, G820R,
861 13 N861H, N861I,
770 13
55 13 S55L,
779 13
821 13 D821E, D821E,
12 13 N12D,
831 13
857 13 E857X,
30 14 I30Del, I30T,
40 14
29 14 F29L, F29V, F29S, F29L, F29L,
819 14 N819K, N819K,
13 14 T13N,
32 14 A32T
767 14 D767X,
49 15 C49R, C49G,
794 15 V794I, V794D,
768 15
761 15
766 15
791 15 R791W, R791Q,
765 15
740 15 C740G, C740W,
764 15
736 15