KCNH2 Variant R92L

Summary of observed carriers, functional annotations, and structural context for KCNH2 R92L. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT2 penetrance

11%

90% CI: 0.9% – 28.5%

1/11 effective observations

Total carriers

1

0 LQT2 · 1 unaffected

Functional studies

0

Publications with functional data

R92L is present in 1 alleles in gnomAD. This residue resides in a Mild_Hotspot region for LQT2.

We have tested the trafficking efficiency of this variant: 85% of WT with a standard error of 12%. 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 1 individuals with LQT2 and 9 unaffected individuals.

In silico predictors

Variant-level computational predictors.
PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density LQT2 (%)
-3.575 0.009 -3 0.502 22

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
Literature, cohort, and gnomAD – 1 1 0 –
Variant features alone – 10 9 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. 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 R92L.
Neighbour residue Distance (Å) Observed variants
92 0 R92C, R92L,
90 5 E90K,
85 5 A85P, A85V,
91 6
112 6 V112M,
94 7 V94L, V94L, V94A,
93 7 K93X, K93R,
81 7 Q81E, Q81X, Q81P, Q81H, Q81H,
89 8 A89G, A89V,
88 8
82 8 I82Del, I82dup, I82Ins, I82T,
84 8
111 9 D111V,
86 9 L86R,
110 9 V110A,
113 9 V113Del,
114 9 P114S,
83 9 A83P, A83fsX,
87 10 L87P,
80 11 A80P,
78 12 A78T, A78P,
125 12
109 12 L109X, L109Q, L109P,
127 12
79 12 A79T, A79S, A79Del, A79fsX,
95 12 E95K, E95G,
126 13
128 13 N128S,
77 13 R77S,
96 13 I96V, I96T,
122 14
115 14 V115M,
64 14 C64R, C64Y,
65 14 T65P,
116 14 K116Q,
129 14 F129C
108 15 C108Y,