KCNQ1 Variant T501A

Summary of observed carriers, functional annotations, and structural context for KCNQ1 T501A. Data combine curated literature, international cohorts, and gnomAD observations.

Estimated LQT1 penetrance

8%

0/12 effective observations

Total carriers

2

0 LQT1 · 2 unaffected

Functional studies

0

Publications with functional data

T501A is present in 2 alleles in gnomAD. This residue resides in a Non_Hotspot region for LQT1.

Variant features alone are equivalent to phenotyping 0 individuals with LQT1 and 10 unaffected individuals.

In silico predictors

Variant-level computational predictors.
PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density LQT1 (%)
-1.17 0.052 1 0.681 1

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 10 0 –

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 T501A.
Neighbour residue Distance (Å) Observed variants
501 0 T501A,
500 4 I500L, I500V,
502 4
499 5 P499S,
503 5
498 7
504 7
497 8 L497P,
505 8 Q505R,
496 8
506 8
495 9 T495S, T495S, T495A,
507 9 R507Q, R507W,
494 10
508 10 E508G,
493 11 G493A,
509 11 H509Q, H509Q, H509R,
492 11 L492ins,
510 11 H510R, H510Y,
491 12
511 12 R511Q, R511W,
490 13
512 13
489 13
513 13 T513A, T513S, T513S
488 14 D488E, D488E,
514 14 I514T,
487 14 E487K,
515 14
486 15 A486T,
516 15