KCNH2 Variant R537G Detail

We estimate the penetrance of LQTS for KCNH2 R537G is 17%. We are unaware of any observations of this variant in individuals. R537G is not present in gnomAD. We have tested the trafficking efficiency of this variant, 89% of WT with a standard error of 20%; in our analysis we used SE < 20% as 'high quality'. Approximately below 50% of WT is considered PS3 moderate and below 30% is PS3 strong. R537G has not been functionally characterized. 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 1 individuals with LQT2 and 9 unaffected individuals.These data combined with observations of carriers lead us to estimate the LQTS penetrance for KCNQ1 R537G around 17% (1/10).

In Silico Data

PROVEAN PolyPhen-2 BLAST-PSSM REVEL Penetrance Density (%)
-6.709 0.999 -3 0.753 59
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
LITERATURE, COHORT, AND GNOMAD: - 0 0 0 -
VARIANT FEATURES ALONE: - 10 9 1 -
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.

R537G has 52 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
537 0 R537W,
538 4
497 5 W497X, W497L,
536 5 A536X,
534 6 R534C,
533 6
535 7 V535M,
501 8 D501Y, D501H, D501N,
539 9
496 9
470 9 N470D,
493 10 Y493C, Y493H, Y493Ins, Y493F,
500 10 I500Del,
532 10
540 10 D540fsX,
411 10
542 10
466 11 D466E, D466E,
541 11 R541C, R541H,
414 11 I414fsX,
498 11
492 11 H492Y,
530 11
407 12
467 12
475 12 Y475C, Y475Del,
415 12
531 12 R531W, R531Del, R531Q,
499 12
418 12
3 13
473 13 T473P,
476 13 V476I,
463 13 F463L, F463L, F463L,
402 13 H402R,
469 13
502 13 M502I, M502I, M502I,
410 13 W410X,
474 13 T474I,
504 13 A504V,
543 14 S543fsX,
471 14 F471X,
408 14
412 14 W412X,
4 14
495 14 K495X,
494 14 F494Del,
489 14 I489F, I489I,
503 14
417 15
529 15
477 15