A rigorous in silico genomic interrogation at 1p13.3 reveals 16 autosomal dominant candidate genes in syndromic neurodevelopmental disorders

Afif Ben-Mahmoud, Kyung Ran Jun, Vijay Gupta, Pinang Shastri, Alberto de la Fuente, Yongsoo Park, Kyung Chul Shin, Chong Ae Kim, Aparecido Divino da Cruz, Irene Plaza Pinto, Lysa Bernardes Minasi, Alex Silva da Cruz, Laurence Faivre, Patrick Callier, Caroline Racine, Lawrence C. Layman, Il Keun Kong, Cheol Hee Kim, Woo Yang Kim, Hyung Goo Kim

Research output: Contribution to journalArticlepeer-review


Genome-wide chromosomal microarray is extensively used to detect copy number variations (CNVs), which can diagnose microdeletion and microduplication syndromes. These small unbalanced chromosomal structural rearrangements ranging from 1 kb to 10 Mb comprise up to 15% of human mutations leading to monogenic or contiguous genomic disorders. Albeit rare, CNVs at 1p13.3 cause a variety of neurodevelopmental disorders (NDDs) including development delay (DD), intellectual disability (ID), autism, epilepsy, and craniofacial anomalies (CFA). Most of the 1p13.3 CNV cases reported in the pre-microarray era encompassed a large number of genes and lacked the demarcating genomic coordinates, hampering the discovery of positional candidate genes within the boundaries. In this study, we present four subjects with 1p13.3 microdeletions displaying DD, ID, autism, epilepsy, and CFA. In silico comparative genomic mapping with three previously reported subjects with CNVs and 22 unreported DECIPHER CNV cases has resulted in the identification of four different sub-genomic loci harboring five positional candidate genes for DD, ID, and CFA at 1p13.3. Most of these genes have pathogenic variants reported, and their interacting genes are involved in NDDs. RT-qPCR in various human tissues revealed a high expression pattern in the brain and fetal brain, supporting their functional roles in NDDs. Interrogation of variant databases and interacting protein partners led to the identification of another set of 11 potential candidate genes, which might have been dysregulated by the position effect of these CNVs at 1p13.3. Our studies define 1p13.3 as a genomic region harboring 16 NDD candidate genes and underscore the critical roles of small CNVs in in silico comparative genomic mapping for disease gene discovery. Our candidate genes will help accelerate the isolation of pathogenic heterozygous variants from exome/genome sequencing (ES/GS) databases.

Original languageEnglish (US)
Article number979061
JournalFrontiers in Molecular Neuroscience
StatePublished - Oct 6 2022


  • 1p13.3 deletion
  • GSTM5
  • LRIF1
  • VAV3
  • WDR47
  • autism
  • intellectual disability

ASJC Scopus subject areas

  • Molecular Biology
  • Cellular and Molecular Neuroscience


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