Description
Variant summary: KCNH2 c.2371C>T (p.Arg791Trp) results in a non-conservative amino acid change located in the Cyclic nucleotide-binding domain (IPR000595) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8.9e-05 in 281704 control chromosomes, predominantly at a frequency of 0.00093 within the African or African-American subpopulation in the gnomAD database. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 8 fold of the estimated maximal expected allele frequency for a pathogenic variant in KCNH2 causing Long QT Syndrome phenotype (0.00012), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African or African-American origin. c.2371C>T has been reported in the literature in individuals affected with Long QT Syndrome and sudden infant death syndrome (Kapplinger_2009, Smith_2018), however without strong evidence for causality (e.g., lack of co-segregation data). These reports therefore do not provide unequivocal conclusions about association of the variant with Long QT Syndrome. One functional study showed this variant with competent trafficking and moderate alteration on gating (Anderson_2014) with nearly normal values for the repolarizing outward potassium current density or Ikv11.1. Another functional study demonstrated this variant expressed and generated peak Kv11.1 current levels similar to cells expressing wild-type-Kv11.1 channels but altered gating (Smith_2018). The following publications have been ascertained in the context of this evaluation (PMID: 25637381, 25417810, 32048431, 19716085, 29247119, 26332594, 29752375). ClinVar contains an entry for this variant (Variation ID: 67391). Based on the evidence outlined above, the variant was classified as likely benign.
# | Sample | Method | Observation |
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Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences |
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1 | germline | unknown | not provided | not provided | not provided | | not provided | not provided | not provided | not provided |