Conflicting Genotype-Phenotype Data on ITSN1 as a Candidate Gene for Neurodevelopmental Disorders
Laboratory Genetics and Genomics
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Primary Categories:
- Laboratory Genetics
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Secondary Categories:
- Laboratory Genetics
Introduction
Though advancements in next generation sequencing have enhanced our understanding and detection of Mendelian neurodevelopmental disorders (NDD), approximately 60% of individuals with this phenotype remain undiagnosed after genetic testing. Recently, intersectin 1 (ITSN1), a gene with de novo variants identified through large-scale, genomic screens for candidates in patients with NDD, has been implicated in autosomal dominant autism, intellectual disability, and epilepsy in two studies. Null variants and missense variants clustering in the C-terminal region have been proposed as disease mechanisms, with developmental regression, speech loss, and seizures as the main clinical features. However, the phenotypic and mutational spectrum remain incompletely understood, and gene-disease validity is still being established.
Case Presentation
A 4-year-old girl had autism and regression of developmental milestones (notably speech loss at 18 months), stereotypic hand movements, and a history of staring spells. Family history was non-contributory. Previous testing for Fragile X syndrome was negative.
Diagnostic Workup
Exome sequencing (ES) for the analysis of a panel of genes related to autism and developmental delays was performed. In addition, we analyzed the entire exome for additional, high-impact candidate variants that might underlie the patient’s phenotype.
A heterozygous likely pathogenic nonsense variant was found in ITSN1: NM_003024(ITSN1):c.934C>T (p.Arg312Ter). Parental testing for the presence of this variant was performed and neither parent was found to carry the ITSN1 p.Arg312Ter variant in DNA isolated from peripheral blood, consistent with this change representing a de novo variant, allowing for reclassification of this variant as pathogenic.
Discussion
A search of our internal database identified two patients with putative ITSN1 null variants. Unexpectedly, both had normal development. The first patient, an 11-year-old male with retinitis pigmentosa harbored a frameshift variant in exon 25 (ITSN1 c.3155_3158del, p.S1052fs), theoretically resulting in loss-of-function, most likely through nonsense-mediated mRNA decay. The second patient is a 9-year-old male who was originally tested due to suspicion of MCAD deficiency but is now healthy and developmentally normal and harbored a splice variant (ITSN1 c.2319+2dupT), predicted to cause an in-frame deletion of 5 amino acids through exon skipping in exon 20, though functional studies have not been performed. Notably, both variants were located outside the missense-constrained region of ITSN1, raising questions about the pathogenicity of null variants and in-frame copy number variants in certain regions.
Approximately a dozen individuals with ITSN1-associated NDD have been described in current literature. Though most reported cases involve a de novo change, inheritance from paucisymptomatic individuals has been described. The ITSN1 gene, located at chromosome 21q22.11, is evolutionarily conserved and encodes a multidomain protein involved in important cellular processes including endo- and exocytosis, mitogenic signaling, apoptosis, and cytoskeleton rearrangements. Two isoforms have been described: a ubiquitous short isoform, and a long isoform that is predominantly expressed in neurons. Recent studies in mammalian models show evidence for important roles in brain development. Though a clear genotype-phenotype correlation does not currently exist, the location and type of genomic change appears to influence disease development. In the future, additional cases should help clarify the mutational spectrum in ITSN1-related NDD, which may provide information regarding genotype-phenotype correlation.
Conclusion
Our findings help further define the phenotypic and mutational spectrum of ITSN1-associated disorders. The identification of patients with null variants and normal development highlights the complexity of genotype-phenotype correlations in ITSN1 and underscores the need for further parental studies, functional studies, and careful interpretation of variants to refine the mutational spectrum and improve diagnostic accuracy.
Though advancements in next generation sequencing have enhanced our understanding and detection of Mendelian neurodevelopmental disorders (NDD), approximately 60% of individuals with this phenotype remain undiagnosed after genetic testing. Recently, intersectin 1 (ITSN1), a gene with de novo variants identified through large-scale, genomic screens for candidates in patients with NDD, has been implicated in autosomal dominant autism, intellectual disability, and epilepsy in two studies. Null variants and missense variants clustering in the C-terminal region have been proposed as disease mechanisms, with developmental regression, speech loss, and seizures as the main clinical features. However, the phenotypic and mutational spectrum remain incompletely understood, and gene-disease validity is still being established.
Case Presentation
A 4-year-old girl had autism and regression of developmental milestones (notably speech loss at 18 months), stereotypic hand movements, and a history of staring spells. Family history was non-contributory. Previous testing for Fragile X syndrome was negative.
Diagnostic Workup
Exome sequencing (ES) for the analysis of a panel of genes related to autism and developmental delays was performed. In addition, we analyzed the entire exome for additional, high-impact candidate variants that might underlie the patient’s phenotype.
A heterozygous likely pathogenic nonsense variant was found in ITSN1: NM_003024(ITSN1):c.934C>T (p.Arg312Ter). Parental testing for the presence of this variant was performed and neither parent was found to carry the ITSN1 p.Arg312Ter variant in DNA isolated from peripheral blood, consistent with this change representing a de novo variant, allowing for reclassification of this variant as pathogenic.
Discussion
A search of our internal database identified two patients with putative ITSN1 null variants. Unexpectedly, both had normal development. The first patient, an 11-year-old male with retinitis pigmentosa harbored a frameshift variant in exon 25 (ITSN1 c.3155_3158del, p.S1052fs), theoretically resulting in loss-of-function, most likely through nonsense-mediated mRNA decay. The second patient is a 9-year-old male who was originally tested due to suspicion of MCAD deficiency but is now healthy and developmentally normal and harbored a splice variant (ITSN1 c.2319+2dupT), predicted to cause an in-frame deletion of 5 amino acids through exon skipping in exon 20, though functional studies have not been performed. Notably, both variants were located outside the missense-constrained region of ITSN1, raising questions about the pathogenicity of null variants and in-frame copy number variants in certain regions.
Approximately a dozen individuals with ITSN1-associated NDD have been described in current literature. Though most reported cases involve a de novo change, inheritance from paucisymptomatic individuals has been described. The ITSN1 gene, located at chromosome 21q22.11, is evolutionarily conserved and encodes a multidomain protein involved in important cellular processes including endo- and exocytosis, mitogenic signaling, apoptosis, and cytoskeleton rearrangements. Two isoforms have been described: a ubiquitous short isoform, and a long isoform that is predominantly expressed in neurons. Recent studies in mammalian models show evidence for important roles in brain development. Though a clear genotype-phenotype correlation does not currently exist, the location and type of genomic change appears to influence disease development. In the future, additional cases should help clarify the mutational spectrum in ITSN1-related NDD, which may provide information regarding genotype-phenotype correlation.
Conclusion
Our findings help further define the phenotypic and mutational spectrum of ITSN1-associated disorders. The identification of patients with null variants and normal development highlights the complexity of genotype-phenotype correlations in ITSN1 and underscores the need for further parental studies, functional studies, and careful interpretation of variants to refine the mutational spectrum and improve diagnostic accuracy.