KCNH2 Variant L109Q

Summary of observed carriers, functional annotations, and structural context for KCNH2 L109Q. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT2 penetrance

18%

90% CI: 3.4% – 38.6%

1/11 effective observations

Total carriers

1

0 LQT2 · 1 unaffected

Functional studies

0

Publications with functional data

L109Q is present in 1 alleles in gnomAD. This residue resides in a Hotspot region for LQT2.

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 (%)
-2.284 0.015 -1 0.737 53

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 L109Q.
Neighbour residue Distance (Å) Observed variants
109 0 L109X, L109Q, L109P,
110 4 V110A,
108 5 C108Y,
95 6 E95K, E95G,
93 6 K93X, K93R,
130 6 E130K,
94 6 V94L, V94L, V94A,
111 6 D111V,
129 7 F129C,
131 7 V131L, V131L, V131fsX,
128 8 N128S,
107 8 L107P,
96 8 I96V, I96T,
112 10 V112M,
98 10
28 10 K28E,
127 10
97 10
106 10 F106L, F106V, F106L, F106L,
82 11 I82Del, I82dup, I82Ins, I82T,
91 11
92 12 R92C, R92L,
78 12 A78T, A78P,
81 12 Q81E, Q81X, Q81P, Q81H, Q81H,
113 12 V113Del,
51 12
27 13 R27X, R27P,
126 13
29 13 F29L, F29V, F29S, F29L, F29L,
79 13 A79T, A79S, A79Del, A79fsX,
48 13
30 13 I30Del, I30T
69 14 L69Del, L69P,
105 14
85 14 A85P, A85V,
75 14 Q75X,
74 14 T74fsX, T74M,
66 15 C66R, C66G, C66Y,
90 15 E90K,
70 15 H70R, H70Q, H70Q,
47 15 G47C, G47V,
22 15 F22Y, F22S,
25 15 Q25P,
26 15 S26I,