KCNQ1 Variant R109C

Summary of observed carriers, functional annotations, and structural context for KCNQ1 R109C. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT1 penetrance

12%

1/12 effective observations

Total carriers

2

0 LQT1 · 2 unaffected

Functional studies

0

Publications with functional data

R109C is present in 2 alleles in gnomAD. This residue resides in a Non_Hotspot region for LQT1.

Variant features alone are equivalent to phenotyping 1 individuals with LQT1 and 9 unaffected individuals.

In silico predictors

Variant-level computational predictors.
PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density LQT1 (%)
-3.96 0.837 0 0.726 5

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 LQT1 Other Disease
Literature, cohort, and gnomAD – 2 2 0 –
Variant features alone – 15 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.

Previously observed variants near R109C.
Neighbour residue Distance (Å) Observed variants
109 0 R109C, R109L,
106 5
108 5 G108S,
105 6
110 6 V110I,
107 8 Q107H, Q107H,
112 8
113 9
104 9 T104A, T104I
180 10
111 10 Y111C,
177 11 S177F,
121 11
122 11 C122Y,
114 11
119 12 G119R, G119V,
116 12
118 12
117 12 P117L,
179 13 G179S,
173 13
115 13 E115A, E115G,
178 13 A178T, A178del,
181 14 R181C,
176 14
174 14 R174H, R174C, R174L,
125 15