KCNQ1 Variant S143Y

Summary of observed carriers, functional annotations, and structural context for KCNQ1 S143Y. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT1 penetrance

55%

6/11 effective observations

Total carriers

1

0 LQT1 · 1 unaffected

Functional studies

0

Publications with functional data

S143Y is present in 1 alleles in gnomAD. This residue resides in a Hotspot region for LQT1.

Variant features alone are equivalent to phenotyping 6 individuals with LQT1 and 4 unaffected individuals.

In silico predictors

Variant-level computational predictors.
PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density LQT1 (%)
-5.43 1.0 0 0.838 61

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 – 1 1 0 –
Variant features alone – 15 4 6 –

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 S143Y.
Neighbour residue Distance (Å) Observed variants
143 0 S143F, S143P, S143Y,
144 4 T144A,
140 5 S140G, S140R, S140R, S140R,
142 5
149 5
145 6
141 6 V141M,
152 6
148 7
153 7 T153M,
146 7 E146K, E146G, E146Q,
139 7
231 8 R231C, R231H, R231S,
156 8
150 9 A150T,
147 9 Q147R,
138 9
299 10
298 10 S298I, S298N,
151 10
227 10
155 10
136 10
154 10
137 10 L137F, L137P,
230 11
234 11 Q234H, Q234H,
300 11 A300T, A300S,
281 11 Y281C
297 11 G297S, G297D, G297R,
226 11 A226V,
160 12 E160del, E160K, E160V,
135 12
159 12 M159del,
228 12
157 13 F157C,
229 13 G229D,
285 13
222 13
301 13
303 14 L303P,
217 14
235 14 I235N,
302 14 A302V, A302E, A302T,
278 14 Y278H,
225 14 S225L, S225del,
233 14 L233P,
223 14
134 15 L134P,
232 15
133 15 V133I,