A massively parallel assay accurately discriminates between functionally normal and abnormal variants in a hotspot domain of KCNH2.
PAS domain
automated patch clamp
deep mutational scanning
functional genomics
hERG
long QT syndrome
mutational hotspot
Journal
American journal of human genetics
ISSN: 1537-6605
Titre abrégé: Am J Hum Genet
Pays: United States
ID NLM: 0370475
Informations de publication
Date de publication:
07 07 2022
07 07 2022
Historique:
received:
10
01
2022
accepted:
03
05
2022
pubmed:
11
6
2022
medline:
14
7
2022
entrez:
10
6
2022
Statut:
ppublish
Résumé
Many genes, including KCNH2, contain "hotspot" domains associated with a high density of variants associated with disease. This has led to the suggestion that variant location can be used as evidence supporting classification of clinical variants. However, it is not known what proportion of all potential variants in hotspot domains cause loss of function. Here, we have used a massively parallel trafficking assay to characterize all single-nucleotide variants in exon 2 of KCNH2, a known hotspot for variants that cause long QT syndrome type 2 and an increased risk of sudden cardiac death. Forty-two percent of KCNH2 exon 2 variants caused at least 50% reduction in protein trafficking, and 65% of these trafficking-defective variants exerted a dominant-negative effect when co-expressed with a WT KCNH2 allele as assessed using a calibrated patch-clamp electrophysiology assay. The massively parallel trafficking assay was more accurate (AUC of 0.94) than bioinformatic prediction tools (REVEL and CardioBoost, AUC of 0.81) in discriminating between functionally normal and abnormal variants. Interestingly, over half of variants in exon 2 were found to be functionally normal, suggesting a nuanced interpretation of variants in this "hotspot" domain is necessary. Our massively parallel trafficking assay can provide this information prospectively.
Identifiants
pubmed: 35688148
pii: S0002-9297(22)00209-9
doi: 10.1016/j.ajhg.2022.05.003
pmc: PMC9300756
pii:
doi:
Substances chimiques
ERG1 Potassium Channel
0
Ether-A-Go-Go Potassium Channels
0
KCNH2 protein, human
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Research Support, N.I.H., Extramural
Langues
eng
Sous-ensembles de citation
IM
Pagination
1208-1216Subventions
Organisme : NHLBI NIH HHS
ID : R00 HL135442
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL160863
Pays : United States
Informations de copyright
Copyright © 2022 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests The authors declare no competing interests.
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