KCNH2 Variant E58D

Summary of observed carriers, functional annotations, and structural context for KCNH2 E58D. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT2 penetrance

22%

90% CI: 9.7% – 52.4%

3/11 effective observations

Total carriers

1

1 LQT2 · 0 unaffected

Functional studies

1

Publications with functional data

E58D has not been reported in gnomAD. This residue resides in a Hotspot region for LQT2.

We have tested the trafficking efficiency of this variant: 70% of WT with a standard error of 20%. In our analysis we used SE < 20% as 'high quality'. Approximately below 50% of WT is considered PS3 moderate and below 30% is PS3 strong.

Variant features alone are equivalent to phenotyping 2 individuals with LQT2 and 8 unaffected individuals.

In silico predictors

Variant-level computational predictors.
PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density LQT2 (%)
-0.667 0.0 4 0.659 80

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
Italy Cohort 2020 1 0 1
Literature, cohort, and gnomAD – 1 0 1 –
Variant features alone – 10 8 2 –

Totals may differ from individual publications due to duplicate patients removed during curation.

Functional data

Functional assay results from published electrophysiology studies. Steady state (S.S.) and peak tail current are relative % to wildtype (100% being no different from wildtype). V1/2 activation and inactivation are the voltages at which half of the maximal current is reached, in mV. Recovery from inactivation and deactivation time are ratios of characteristic time constants with wildtype. HM indicates homomeric channels, HT indicates heteromeric channels.

Homomeric channel data

Published electrophysiology measurements (homomeric).
PubMed ID Cell Type S.S Peak (%WT) Peak Tail IKr (%WT) V1/2 Act. V1/2 Inact. Recov. Inact. Deactivation (%WT)
25417810 HEK293 64 -0.5 None None 0.893413174

Heteromeric channel data

Published electrophysiology measurements (heteromeric).
PubMed ID Cell Type S.S Peak (%WT) Peak Tail IKr (%WT) V1/2 Act. V1/2 Inact. Deactivation (%WT)
25417810 HEK293 None None None

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 E58D.
Neighbour residue Distance (Å) Observed variants
58 0 E58K, E58D, E58D,
57 4 A57P,
55 4 S55L,
54 5 Y54N, Y54X,
59 5
62 7 R62Q,
60 8 M60T,
68 8 F68L, F68V, F68L, F68L,
857 8 E857X,
53 8 G53S, G53R,
101 9 K101E,
56 9 R56Q,
52 10 C52W,
49 10 C49R, C49G,
61 10 Q61R,
859 10 T859M, T859R,
44 10 C44F, C44X, C44W,
858 11 I858V, I858T,
48 11
41 11 V41A,
69 11 L69Del, L69P,
66 12 C66R, C66G, C66Y,
860 12
63 12 P63H,
861 12 N861H, N861I,
67 13
856 13
855 14 S855R, S855R, S855R,
854 14
804 14
40 14
51 14
102 14 D102H, D102V, D102X,
30 14 I30Del, I30T
100 14 R100G, R100Q, R100P,
45 14 N45D, N45K, N45K,
46 14 D46Y, D46E, D46E,
43 14 Y43D, Y43C,
803 14 D803Y, D803X,
741 14 K741R,
42 14 I42N,
50 14 E50X,
47 15 G47C, G47V,
64 15 C64R, C64Y,