A novel framework for functional annotation of variants of uncertain significance in ID/ASD risk gene CC2D1A

Authors

Aniket Bhattacharya, Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States.
Paola Parlanti, Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States.
Luca Cavallo, Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States.
Edward Farrow, Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, 2121 I St NW, Washington, DC 20052, United States.
Tyler Spivey, Department of Pharmacology and Physiology, School of Medicine and Health Sciences, George Washington University, 2121 I St NW, Washington, DC 20052, United States.
Alessandra Renieri, Medical Genetics, University of Siena, Viale Bracci 2, 53100 Siena, Italy.
Francesca Mari, Medical Genetics, University of Siena, Viale Bracci 2, 53100 Siena, Italy.
M Chiara Manzini, Child Health Institute of New Jersey and Department of Neuroscience and Cell Biology, Rutgers - Robert Wood Johnson Medical School, 89 French Street, New Brunswick, NJ 08901, United States.

Document Type

Journal Article

Publication Date

4-23-2024

Journal

Human molecular genetics

DOI

10.1093/hmg/ddae070

Keywords

CC2D1A; CREB; VUS; autism; intellectual disability

Abstract

Intellectual disability (ID) and autism spectrum disorder (ASD) are genetically heterogeneous with hundreds of identified risk genes, most affecting only a few patients. Novel missense variants in these genes are being discovered as clinical exome sequencing is now routinely integrated into diagnosis, yet most of them are annotated as variants of uncertain significance (VUS). VUSs are a major roadblock in using patient genetics to inform clinical action. We developed a framework to characterize VUSs in Coiled-coil and C2 domain containing 1A (CC2D1A), a gene causing autosomal recessive ID with comorbid ASD in 40% of cases. We analyzed seven VUSs (p.Pro319Leu, p.Ser327Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, p.Arg886His and p.Glu910Lys) from four cases of individuals with ID and ASD. Variants were cloned and overexpressed in HEK293 individually and in their respective heterozygous combination. CC2D1A is a signaling scaffold that positively regulates PKA-CREB signaling by repressing phosphodiesterase 4D (PDE4D) to prevent cAMP degradation. After testing multiple parameters including direct interaction between PDE4D and CC2D1A, cAMP levels and CREB activation, we found that the most sensitive readout was CREB transcriptional activity using a luciferase assay. Compared to WT CC2D1A, five VUSs (p.Pro319Leu, p.Gly441Val, p.Val449Met, p.Thr580Ile, and p.Arg886His) led to significantly blunted response to forskolin induced CREB activation. This luciferase assay approach can be scaled up to annotate ~150 CC2D1A VUSs that are currently listed in ClinVar. Since CREB activation is a common denominator for multiple ASD/ID genes, our paradigm can also be adapted for their VUSs.

APA Citation

Bhattacharya, Aniket; Parlanti, Paola; Cavallo, Luca; Farrow, Edward; Spivey, Tyler; Renieri, Alessandra; Mari, Francesca; and Manzini, M Chiara, "A novel framework for functional annotation of variants of uncertain significance in ID/ASD risk gene CC2D1A" (2024). GW Authored Works. Paper 4686.
https://hsrc.himmelfarb.gwu.edu/gwhpubs/4686

Department

School of Medicine and Health Sciences Student Works