KCNH2 Variant L559H Detail

We estimate the penetrance of LQTS for KCNH2 L559H is 80%. This variant was found in a total of 4 carriers in 3 papers or gnomAD, 4 had LQTS. L559H is not present in gnomAD. L559H has been functionally characterized in 1 papers. This residue is located in a Hotspot region for LQT2. In silico predictions, functional data (if available), and location in structure are equivalent to observing 7 individuals with LQT2 and 3 unaffected individuals.These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 L559H around 80% (11/14).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-6.709 1.0 -3 0.984 80
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 LQT2 Other Disease
24667783 2015 1 0 1
12442276 2002 2 0 2
26496715 2015 1 0 1
LITERATURE, COHORT, AND GNOMAD: - 4 0 4 -
VARIANT FEATURES ALONE: - 10 3 7 -
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

Steady state (S.S.) and peak tail current are relative % to wildtype (100% being no different from wildtype). V0.5 act/inact are the voltages at which half of the maximal current is reached during an activation and inactivation protocol, each is 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 S.S Peak (%WT) Peak Tail IKr (%WT) V1/2 Act. V1/2 Inact. Recov. Inact. Deactivation (%WT)
18218237 HEK293 None None None None

Functional Data Heterozygously Collected

Functional parameters are the same as defined above.

PubMed ID Cell Type S.S Peak (%WT) Peak Tail IKr (%WT) V1/2 Act. V1/2 Inact. Deactivation (%WT)
18218237 HEK293 100 None None None

L559H has 55 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 since the functional KV11.1 channel (protein product of KCNH2/hERG) 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
559 0 L559F, L559H,
558 4 A558P, A558V, A558E,
560 5 I560fsX, I560M,
563 5 W563C, W563G, W563X, W563C,
556 5
562 5 H562Q, H562P, H562R, H562Q,
555 6
561 6 A561P, A561T, A561V,
422 6 A422T,
423 7
419 7
557 8
564 9 L564L,
426 10 P426H,
554 10
532 10
421 10 T421M, T421fsX,
552 10 L552S,
565 10
418 10
619 10
566 10 C566F, C566S, C566G, C566R, C566S,
615 10 L615V, L615F,
529 11
553 11 L553V,
424 11
425 11
618 11 T618S, T618S,
551 11 F551L, F551L, F551L,
651 12 M651K,
420 12 Y420C,
611 12 Y611D,
415 12
622 12 L622F,
646 12
567 12 I567M, I567T,
655 13
427 13 Y427C, Y427S, Y427H,
416 13
535 13 V535M,
647 13
642 13 I642V, I642Del,
614 14 A614V, A614T,
417 14
648 14 G648A,
644 14 V644F, V644I,
531 14 R531Q, R531W, R531Del,
550 14
533 14
656 14 F656L, F656L, F656L,
428 15 S428fsX, S428X, S428L,
530 15
526 15
623 15 T623I,
612 15 V612A, V612L, V612L,