KCNH2 Variant P72Q

Summary of observed carriers, functional annotations, and structural context for KCNH2 P72Q. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT2 penetrance

60%

90% CI: 40.6% – 76.8%

11/19 effective observations

Total carriers

9

8 LQT2 · 1 unaffected

Functional studies

0

Publications with functional data

P72Q has not been reported in gnomAD. This residue resides in a Hotspot region for LQT2.

We have tested the trafficking efficiency of this variant: 66% 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 3 individuals with LQT2 and 7 unaffected individuals.

In silico predictors

Variant-level computational predictors.
PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density LQT2 (%)
-3.171 0.822 -1 0.789 82

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 2 1 1
11854117 2002 7 0 7
10973849 2000 2 0 2
Literature, cohort, and gnomAD – 9 1 8 –
Variant features alone – 10 7 3 –

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 P72Q.
Neighbour residue Distance (Å) Observed variants
72 0 P72T, P72S, P72Q, P72R,
71 3 G71R, G71R, G71W, G71E,
73 4 R73G, R73C, R73fsX, R73H,
74 5 T74fsX, T74M,
99 7 Y99N, Y99S,
70 8 H70R, H70Q, H70Q,
75 9 Q75X,
97 9
105 9
103 10
98 11
76 11
69 11 L69Del, L69P,
96 11 I96V, I96T,
104 12
106 12 F106L, F106V, F106L, F106L,
67 12
78 13 A78T, A78P,
79 13 A79T, A79S, A79Del, A79fsX,
100 13 R100G, R100Q, R100P,
68 13 F68L, F68V, F68L, F68L,
107 14 L107P
77 14 R77S,
102 14 D102H, D102V, D102X,
66 15 C66R, C66G, C66Y,