KCNQ1 Variant G189R Detail

We estimate the penetrance of LQTS for KCNQ1 G189R is 57%. This variant was found in a total of 9 carriers in 5 papers or gnomAD, 6 had LQTS. G189R is not present in gnomAD. G189R has been functionally characterized in 2 papers. This residue is located in a Hotspot region for LQT1. In silico predictions, functional data (if available), and location in structure are equivalent to observing 4 individuals with LQT1 and 6 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 G189R around 57% (10/19).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-7.38 1.0 -1 0.967 57
PROVEAN scores less than -2 are considered deleterious. REVEL scores higher than 0.5 or 0.75 are considered likely pathogenic (higher sensitivity with the former cutoff, higher specificity with the latter cutoff). A PolyPhen-2 score of 0.85 or greater is considered likely pathogenic. BLAST-PSSM reflects the evolutionary conservation of residue substitutions, more negative numbers indicate fewer observations of the specific substitution than is expected. Penetrance density is our previously published method to calculate the average LQTS probability density in a shell of residues surrounding a residue of interest (Kroncke et al. 2019).

Reported Carrier Data

PubMed ID Year Carriers Unaffected LQT1 Other Disease
32893267 2020 1 None 1 None
30758498 2019 2 None 2 None
19490272 2009 4 None 4 None
17470695 2007 4 None 4 None
10220144 1999 20 3 1 None
Summary totals might not agree with the literature table because of duplicate patients, which were excluded from the total counts. We do not distinguish here between multiple missense codons. Missense variants are combined across degenerate codon substitutions since codon-level data were not consistently available for curation.

Functional Data Homozygously Collected

Peak current is relative to wildtype (100% being no different from wildtype). V0.5 activation is the voltages at which half of the maximal current is reached during an activation in units of mV and relative to wildtype. Recovery from inactivation (Rec. inact.) and deactivation time (Deactivation) are the ratio of characteristic time constants with wildtype (unitless).

PubMed ID Cell Type Peak Current IKs (%WT) V1/2 Act. Activation time (%WT) Deactivation time (%WT)
22456477 HEK None None None
10376919 Oocytes None None None

Functional Data Heterozygously Collected

Functional parameters are the same as defined above.

PubMed ID Cell Type Peak Current IKs (%WT) V1/2 Act. Activation time (%WT) Deactivation time (%WT)
22456477 HEK 75 None None None
10376919 Oocytes 50 0.0 1.0 None

G189R has 32 previously observed neighbors within 15 angstroms

A residue within a folded protein on average has nearest neighbors that fall roughly into two shells: a "nearest" neighbor around 5-6 angstroms and a second shell around 11 angstroms. NOTE: some residues appear multiple times at different distances. This results from the fact that the functional KV7.1 channel is a homotetramer and occasionally the same residue from multiple subunits is present within the 15A window. All variants shown in the rightmost column have been observed in at least one individual in the literature or gnomAD.

Neighbor Distance (Angstroms) Variants Observed in Individuals
189 0 G189R, G189R, G189E,
188 4 W188C, W188C, W188G, W188S,
192 5 R192C, R192H,
190 5 R190W, R190Q, R190L,
186 5 G186R, G186D,
184 5 Y184S, Y184C, Y184D, Y184H,
191 5
185 5 V185L, V185L, V185M, V185del,
187 6 L187P, L187F,
193 7 F193L, F193L, F193L,
183 7 K183R,
178 7 A178T, A178del,
194 8 A194P, A194T,
195 8 R195Q, R195W,
179 9 G179S,
182 9
175 9 L175I,
181 9 R181C,
177 11 S177F,
180 11
196 11
199 12 S199A,
111 13 Y111C,
176 13
171 13
174 14 R174H, R174C, R174L,
200 14
172 14 V172M, V172E,
197 14 P197L,
115 14 E115A, E115G,
107 15 Q107H, Q107H,
173 15