CLTC mutations

 Inspired by a colleague's patient.

DeMari J, Mroske C, Tang S, Nimeh J, Miller R, Lebel RR. CLTC as a clinically novel gene associated with multiple malformations and developmental delay. Am J Med Genet A. 2016 Apr;170A(4):958-66. doi: 10.1002/ajmg.a.37506. Epub 2016 Jan 29. PMID: 26822784.

Abstract

Diagnostic exome sequencing has recently emerged as an invaluable tool in determining the molecular etiology of cases involving dysmorphism and developmental delay that are otherwise unexplained by more traditional methods of genetic testing. Our patient was large for gestational age at 35 weeks, delivered to a 27-year-old primigravid Caucasian whose pregnancy was complicated by preeclampsia. Neonatal period was notable for hypoglycemia, apnea, bradycardia, hyperbilirubinemia, grade I intraventricular hemorrhage, subdural hematoma, laryngomalacia, hypotonia, and feeding difficulties. The patient had numerous minor dysmorphic features. At three and a half years of age, she has global developmental delays and nystagmus, and is being followed for a mediastinal neuroblastoma that is currently in remission. Karyotype and oligo-microarray were normal. Whole-exome, next generation sequencing (NGS) coupled to bioinformatic filtering and expert medical review at Ambry Genetics revealed 14 mutations in 9 genes, and these genes underwent medical review. A heterozygous de novo frameshift mutation, c.2737_2738dupGA p.D913Efs*59, in which two nucleotides are duplicated in exon 17 of the CLTC gene, results in substitution of glutamic acid for aspartic acid at position 913 of the protein, as well as a frame shift that results in a premature termination codon situated 58 amino acids downstream. Clathrin Heavy Chain 1 (CHC1) has been shown to play an important role in the brain for vesicle recycling and neurotransmitter release at pre-synaptic nerve terminals. There is also evidence implicating it in the proper development of the placenta during the early stages of pregnancy. The CLTC alteration identified herein is likely to provide an explanation for the patient's adverse phenotype. Ongoing functional studies will further define the impact of this alteration on CHC1 function and consequently, human disease.

Nabais Sá MJ, Venselaar H, Wiel L, Trimouille A, Lasseaux E, Naudion S, Lacombe D, Piton A, Vincent-Delorme C, Zweier C, Reis A, Trollmann R, Ruiz A, Gabau E, Vetro A, Guerrini R, Bakhtiari S, Kruer MC, Amor DJ, Cooper MS, Bijlsma EK, Barakat TS, van Dooren MF, van Slegtenhorst M, Pfundt R, Gilissen C, Willemsen MA, de Vries BBA, de Brouwer APM, Koolen DA. De novo CLTC variants are associated with a variable phenotype from mild to severe intellectual disability, microcephaly, hypoplasia of the corpus callosum, and epilepsy. Genet Med. 2020 Apr;22(4):797-802. doi: 10.1038/s41436-019-0703-y. Epub 2019 Nov 28. PMID: 31776469.

Abstract

Purpose: To delineate the genotype-phenotype correlation in individuals with likely pathogenic variants in the CLTC gene.

Methods: We describe 13 individuals with de novo CLTC variants. Causality of variants was determined by using the tolerance landscape of CLTC and computer-assisted molecular modeling where applicable. Phenotypic abnormalities observed in the individuals identified with missense and in-frame variants were compared with those with nonsense or frameshift variants in CLTC.

Results: All de novo variants were judged to be causal. Combining our data with that of 14 previously reported affected individuals (n = 27), all had intellectual disability (ID), ranging from mild to moderate/severe, with or without additional neurologic, behavioral, craniofacial, ophthalmologic, and gastrointestinal features. Microcephaly, hypoplasia of the corpus callosum, and epilepsy were more frequently observed in individuals with missense and in-frame variants than in those with nonsense and frameshift variants. However, this difference was not significant.

Conclusions: The wide phenotypic variability associated with likely pathogenic CLTC variants seems to be associated with allelic heterogeneity. The detailed clinical characterization of a larger cohort of individuals with pathogenic CLTC variants is warranted to support the hypothesis that missense and in-frame variants exert a dominant-negative effect, whereas the nonsense and frameshift variants would result in haploinsufficiency.

Martín Fernández-Mayoralas D, Muñoz Jareño N, Alba Menéndez A, Fernández-Jaén A. Periventricular heterotopias: Broadening of the clinical spectrum of the clathrin 1 gene (CLTC) pathogenic variants. Neurologia (Engl Ed). 2021 May;36(4):327-329. English, Spanish. doi: 10.1016/j.nrl.2020.06.008. Epub 2020 Oct 9. PMID: 33041083.