KCNQ1 Variant T444M Detail

We estimate the penetrance of LQTS for KCNQ1 T444M is 8%. This variant was found in a total of 4 carriers in 0 papers or gnomAD, 0 had LQTS. T444M is present in 4 alleles in gnomAD. T444M has been functionally characterized in 1 papers. This residue is located in a Non_Hotspot region for LQT1. In silico predictions, functional data (if available), and location in structure are equivalent to observing 1 individuals with LQT1 and 9 unaffected individuals. These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 T444M around 8% (1/14).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-2.07 1.0 1 0.684 2
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
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)
34930020 HEK 70 3.51 2.02 1.06

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)
34930020 HEK 88 0.17 0.88 0.98

T444M has 31 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
444 0 T444M, T444K,
443 4
445 4
442 5 H442R,
446 5 D446E, D446E, D446E, D446E, D446N,
441 7 P441S,
447 7 P447H,
440 8
448 8 P448R, P448Q, P448L, P448S,
439 8
449 8 E449K,
438 9
450 9 E450K,
437 10 M437V,
451 10 R451Q, R451W,
436 11
452 11 R452Q, R452W, R452L,
435 11
453 11
434 12 G434R, G434R,
454 12
433 13 P433A,
455 13 H455Y, H455Q, H455Q, H455R,
432 13 T432I, T432A,
456 13 F456L, F456L, F456L,
431 14 V431L, V431L,
457 14
430 14
458 14
429 15 N429S,
459 15 D459N, D459V,