KCNH2 Variant V94A

Summary of observed carriers, functional annotations, and structural context for KCNH2 V94A. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT2 penetrance

19%

90% CI: 8.0% – 49.3%

2/11 effective observations

Total carriers

1

1 LQT2 · 0 unaffected

Functional studies

0

Publications with functional data

V94A has not been reported in gnomAD. This residue resides in a Hotspot region for LQT2.

We have tested the trafficking efficiency of this variant: 72% of WT with a standard error of 10%. 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 (%)
-2.318 0.836 0 0.801 77

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
Japan Cohort 2020 1 0 1
Literature, cohort, and gnomAD – 1 0 1 –
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 V94A.
Neighbour residue Distance (Å) Observed variants
94 0 V94L, V94L, V94A,
110 4 V110A,
95 5 E95K, E95G,
81 6 Q81E, Q81X, Q81P, Q81H, Q81H,
93 6 K93X, K93R,
109 6 L109X, L109Q, L109P,
82 6 I82Del, I82dup, I82Ins, I82T,
96 7 I96V, I96T,
78 7 A78T, A78P,
92 7 R92C, R92L,
112 8 V112M,
111 8 D111V,
108 8 C108Y,
79 8 A79T, A79S, A79Del, A79fsX,
85 9 A85P, A85V,
80 9 A80P,
91 10
77 10 R77S,
129 10 F129C,
97 10
98 10
83 10 A83P, A83fsX,
127 11
107 11 L107P,
84 11
75 11 Q75X,
128 11 N128S,
90 11 E90K,
86 12 L86R,
113 12 V113Del,
130 12 E130K,
65 12 T65P,
74 12 T74fsX, T74M,
76 12
131 13 V131L, V131L, V131fsX,
70 13 H70R, H70Q, H70Q,
66 13 C66R, C66G, C66Y,
64 13 C64R, C64Y,
106 14 F106L, F106V, F106L, F106L,
126 14
114 14 P114S,
69 14 L69Del, L69P,
88 14
89 14 A89G, A89V,
125 14
73 14 R73G, R73C, R73fsX, R73H,
30 15 I30Del, I30T
28 15 K28E,
87 15 L87P,