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Rare genetic variants in SEC24D modify orofacial cleft phenotypes
Preprint   Open access

Rare genetic variants in SEC24D modify orofacial cleft phenotypes

Sarah W. Curtis, Jenna C. Carlson, Terri H. Beaty, Jeffrey C. Murray, Seth M. Weinberg, Mary L. Marazita, Justin L. Cotney, David J. Cutler, Michael P. Epstein and Elizabeth J. Leslie
medRxiv
Cold Spring Harbor Laboratory Press, 1.1
03/27/2023
DOI: 10.1101/2023.03.24.23287714
PMCID: PMC10081436
PMID: 37034635
url
https://doi.org/10.1007/s00439-023-02596-4View
Published (Version of record)This article has now been published in a journal and has been peer-reviewed by subject experts. This version may differ significantly from the preprint version. Access restricted to faculty, staff and students
url
https://doi.org/10.1101/2023.03.24.23287714View
Preprint (Author's original)This preprint has not been evaluated by subject experts through peer review. Preprints may undergo extensive changes and/or become peer-reviewed journal articles. Open Access

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Abstract

As one of the most common structural birth defects, orofacial clefts (OFCs) have been studied for decades, and recent studies have demonstrated that there are genetic differences between the different phenotypic presentations of OFCs. However, the contribution of rare genetic variation genome-wide to different subtypes of OFCs has been understudied, with most studies focusing on common genetic variation or rare variation within targeted regions of the genome. Therefore, we used whole-genome sequencing data from the Gabriella Miller Kids First Pediatric Research Program to conduct a gene-based burden analysis to test for genetic modifiers of cleft lip (CL) vs cleft lip and palate (CLP). We found that there was a significantly increased burden of rare variants in SEC24D in CL cases compared to CLP cases (p=6.86×10−7). Of the 15 variants within SEC24D, 53.3% were synonymous, but overlapped a known craniofacial enhancer. We then tested whether these variants could alter predicted transcription factor binding sites (TFBS), and found that the rare alleles destroyed binding sites for 9 transcription factors (TFs), including Pax1 (p=0.0009), and created binding sites for 23 TFs, including Pax6 (p=6.12×10−5) and Pax9 (p= 0.0001), which are known to be involved in normal craniofacial development, suggesting a potential mechanism by which these synonymous variants could have a functional impact. Overall, this study demonstrates that rare genetic variation contributes to the phenotypic heterogeneity of OFCs and suggests that regulatory variation may also contribute and warrant further investigation in future studies of genetic variants controlling risk to OFC.
 Genetic and Genomic Medicine

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