Wednesday, March 30, 2022

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.


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.


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.

Wednesday, March 9, 2022

Even one drink a day could reduce one's overall brain size over time

Daviet R, Aydogan G, Jagannathan K, Spilka N, Koellinger PD, Kranzler HR, Nave G, Wetherill RR. Associations between alcohol consumption and gray and white matter volumes in the UK Biobank. Nat Commun. 2022 Mar 4;13(1):1175. doi: 10.1038/s41467-022-28735-5. PMID: 35246521.


Heavy alcohol consumption has been associated with brain atrophy, neuronal loss, and poorer white matter fiber integrity. However, there is conflicting evidence on whether light-to-moderate alcohol consumption shows similar negative associations with brain structure. To address this, we examine the associations between alcohol intake and brain structure using multimodal imaging data from 36,678 generally healthy middle-aged and older adults from the UK Biobank, controlling for numerous potential confounds. Consistent with prior literature, we find negative associations between alcohol intake and brain macrostructure and microstructure. Specifically, alcohol intake is negatively associated with global brain volume measures, regional gray matter volumes, and white matter microstructure. Here, we show that the negative associations between alcohol intake and brain macrostructure and microstructure are already apparent in individuals consuming an average of only one to two daily alcohol units, and become stronger as alcohol intake increases.

Having even one drink a day could reduce one's overall brain size over time, according to a study published today in the journal Nature Communications.

Why it matters: The study found the greatest risks with heavy drinking, but alcohol consumption was linked to reduced brain volume among far more moderate drinkers. The findings could throw cold water on other studies suggesting that lighter alcohol consumption has no impact on, or may even benefit, the brain.

The analysis by University of Wisconsin and University of Pennsylvania researchers looked at data from 36,000 people who were part of the UK Biobank, a dataset with genetic and medical information from half a million British middle-aged and older adults.

  • The researchers factored such variables as age, height, gender, smoking status and socioeconomic status and corrected for overall head size.
  • Those who drank the most had changes in brain size and function that are associated with cognitive impairments from aging. But the linkage also was evident with moderate drinkers.

What they're saying: "These findings contrast with scientific and governmental guidelines on safe drinking limits," said Henry Kranzler, who directs the Penn Center for Studies of Addiction, in a statement.

  • For example, he pointed out, the National Institute on Alcohol Abuse and Alcoholism recommends women consume an average of no more than one drink per day and men consume no more than two drinks daily on average.
  • "That exceeds the consumption level associated in the study with decreased brain volume," Kranzler said.

The bottom line: This study looked at correlation, not causation. But the size of the data set and the strength of the association should at least give drinkers pause before they call for another round, the researchers said.

Tuesday, March 8, 2022

A single genetic test for 25 tandem repeat disorders

Stevanovski I, Chintalaphani SR, Gamaarachchi H, Ferguson JM, Pineda SS, Scriba CK, Tchan M, Fung V, Ng K, Cortese A, Houlden H, Dobson-Stone C, Fitzpatrick L, Halliday G, Ravenscroft G, Davis MR, Laing NG, Fellner A, Kennerson M, Kumar KR, Deveson IW. Comprehensive genetic diagnosis of tandem repeat expansion disorders with programmable targeted nanopore sequencing. Sci Adv. 2022 Mar 4;8(9):eabm5386. doi: 10.1126/sciadv.abm5386. Epub 2022 Mar 4. PMID: 35245110.


More than 50 neurological and neuromuscular diseases are caused by short tandem repeat (STR) expansions, with 37 different genes implicated to date. We describe the use of programmable targeted long-read sequencing with Oxford Nanopore's ReadUntil function for parallel genotyping of all known neuropathogenic STRs in a single assay. Our approach enables accurate, haplotype-resolved assembly and DNA methylation profiling of STR sites, from a list of predetermined candidates. This correctly diagnoses all individuals in a small cohort (n = 37) including patients with various neurogenetic diseases (n = 25). Targeted long-read sequencing solves large and complex STR expansions that confound established molecular tests and short-read sequencing and identifies noncanonical STR motif conformations and internal sequence interruptions. We observe a diversity of STR alleles of known and unknown pathogenicity, suggesting that long-read sequencing will redefine the genetic landscape of repeat disorders. Last, we show how the inclusion of pharmacogenomic genes as secondary ReadUntil targets can further inform patient care. 


Depending on where they occur, unusually long forms of these repeating sequences can drive neurological or neuromuscular degeneration. Yet because there are 37 known genes that are linked to short tandem repeat disorders, it can take multiple tests before identifying the ones responsible for an individual's symptoms.

For patients like John – one of the participants involved in a new study – it can take over a decade to whittle down the options.

John was ultimately diagnosed with cerebellar ataxia, neuropathy, and vestibular areflexia syndrome, or CANVAS for short. This is a neurodegenerative movement disorder, which is linked to an expansion of repeat DNA sequences in the gene RFC1.

Just in this one gene, however, there are a diversity of ways short DNA sequences can be repeated, which makes a blanket diagnostic test difficult.

"I had test after test for over 10 years and absolutely no answers as to what was wrong,' says John.

Neurologist Kishore Kumar says he and his colleagues at the Garvan Institute for Medical Research in Australia refer to this stressful process as the 'diagnostic odyssey'. As patients like John wait years and years for answers, their symptoms grow gradually worse.

While there's currently no cure for tandem repeat disorders, early diagnosis can help patients manage their symptoms, and hopefully stall some of the disease progression, so the newly developed test should make a big difference to patients.

"This new test will completely revolutionize how we diagnose these diseases, since we can now test for all the disorders at once with a single DNA test and give a clear genetic diagnosis," says Kumar, "helping patients avoid years of unnecessary muscle or nerve biopsies for diseases they don't have, or risky treatments that suppress their immune system."

The newly developed assessment is based on nanopore technology, which can analyze long DNA or RNA fragments in known repetitive regions of the human genome.

Taking a single DNA sample from an individual's blood, researchers can pass the nucleic acids through a protein nanopore, using changes in electrical current arising from the molecular interactions to decode in real time the sequences from 40 genes known to be connected to 25 tandem repeat diseases.

Among 37 patients who were tested using this method, including John, all were correctly matched to their neurogenetic disease.

"We correctly diagnosed all patients with conditions that were already known, including Huntington's disease, fragile X syndrome, hereditary cerebellar ataxias, myotonic dystrophies, myoclonic epilepsies, motor neuron disease, and more," says genomicist Ira Deveson, also from the Garvan Institute.

Current gene sequencing tests require machines as large as fridges, whereas the nanopore technology is no bigger than a stapler. It also costs hundreds of thousands of dollars less, meaning it could be easily scaled up and distributed.

Researchers are now trying to get the method clinically approved. They hope in two to five years the diagnostic test will be used regularly.