Assigning Pathogenicity for TAB2 Variants Using a Novel Scalable Functional Assay and Expanding TAB2 Disease Spectrum

Authors

Weiyi Xu
Andrea Graves
Monika Weisz-Hubshman
Lamees Hegazy
Christina Magyar
Zian Liu
Eleni Nasiotis
Md Abul Hassan Samee
Thomas Burris
Seema Lalani
Lilei Zhang

Publication Date

3-6-2023

Journal

Human Molecular Genetics

DOI

10.1093/hmg/ddac252

PMID

36229919

PMCID

PMC9990987

PubMedCentral® Posted Date

10-14-2022

PubMedCentral® Full Text Version

Post-print

Published Open-Access

yes

Keywords

Humans, Adaptor Proteins, Signal Transducing, Transcription Factor AP-1, Virulence, NF-kappa B, Heart Defects, Congenital

Abstract

Haploinsufficiency of TGF-beta-activated kinase 1 (MAP3K7) binding protein 2 (TAB2) has been associated with congenital heart disease and more recently multiorgan structural abnormalities. Missense variant represents a major proportion of non-synonymous TAB2 variants reported in gnomAD (295/576) and Clinvar (16/73), most of which are variants of uncertain significance (VUSs). However, interpretation of TAB2 missense variants remains challenging because of lack of functional assays. To address this issue, we established a cell-based luciferase assay that enables high-throughput screening of TAB2 variants to assess the functional consequence for predicting variant pathogenicity. Using this platform, we screened 47 TAB2 variants including five pathogenic controls and one benign control, and the results showed that the transcriptional activity of activator protein 1 (AP-1) but not nuclear factor kappa B predicts the TAB2 variant pathogenicity. This assay provides accurate functional readout for both loss-of-function (LOF) and gain-of-function variants, which are associated with distinct phenotypes. In all, 22 out of 32 tested VUSs were reclassified. Genotype-Phenotype association showed that most patients with partial LOF variants do not exhibit congenital heart disease but high frequency of developmental delay, hypotonia and dysmorphic features, which suggests that genetic testing for TAB2 is needed for a broader spectrum of patients with more diverse phenotypes. Molecular modeling with Npl4 zinc finger (NZF) domain variants revealed that the stability of the NZF domain in TAB2 protein is crucial for AP-1 activation. In conclusion, we developed a highly effective functional assay for TAB2 variant prediction and interpretation.

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