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Research Letter
November 16, 2020

Exome Sequencing as a Potential Diagnostic Adjunct in Sporadic Congenital Hydrocephalus

Author Affiliations
  • 1Department of Neurosurgery, Yale School of Medicine, New Haven, Connecticut
  • 2Department of Genetics, Yale University School of Medicine, New Haven, Connecticut
  • 3Department of Genetics, Washington University School of Medicine, St Louis, Missouri
JAMA Pediatr. 2021;175(3):310-313. doi:10.1001/jamapediatrics.2020.4878

Congenital hydrocephalus (CH) affects 1 in 1000 births, is a major cause of morbidity, and costs the US health care system $2 billion annually.1 More than 40% of CH cases are thought to have a genetic etiology. However, only less than 5% of CH cases are associated with a defined gene mutation,1 limiting the utility of genetic testing with targeted approaches and underscoring the need for CH gene discovery. The X-linked recessive form of hydrocephalus associated with aqueductal stenosis (OMIM #307000) owing to mutation of L1 cell adhesion molecule (L1CAM) is the most common form of CH (approximately 3% of total cases),1 and variably presents in male patients with mental retardation, spastic paraparesis, and adducted thumbs as part of L1 syndrome.2 Currently, L1CAM is the only gene for which targeted screening is advised and routinely clinically available for CH; however, there is little consensus on testing criteria or methods.3 Moreover, patients with no family history who present with perinatal CH are most commonly assessed, if at all, by karyotype or microarray analysis aimed at detecting chromosomal abnormalities or copy number variants but unable to identify de novo or inherited rare mutations.4


We applied whole-exome sequencing (WES) to what is, to our knowledge, the largest cohort of neurosurgically treated CH probands collected to date (475 probands and 284 case-parent trios). The structure of our study, in which patients were ascertained on the basis of not having a clinical syndromic or genetic diagnosis from a multitude of institutions largely via a social media approach, enabled a “real-life” snapshot of CH management and allowed us to examine how frequently L1CAM-mutant hydrocephalus is going undiagnosed. The data were collected and analyzed in 2020. Institutional review board approval was provided by Yale University, and all participants provided written consent.


We uncovered 5 novel and 7 total protein-damaging L1CAM mutations (1.47% of our cohort) in male CH probands (Table). Clinical information was available for 6 of 7 patients. Of these 6, all presented with hydrocephalus and aqueductal stenosis diagnosed prenatally (4 or 6) or shortly after birth (2 of 6) with ultrasonography or magnetic resonance imaging. A total of 2 of 7 patients received genetic screens, one of whom was first assessed via microarray-based comparative genomic hybridization at birth, yielding a negative result. The remaining 5 patients harbored mutations that would not have been detected using traditional chromosomal or microarray-based approaches. Novel L1CAM mutations included the p.Trp460Cys and p.Trp635Arg deleterious missense mutations, mapping to the fifth (of 6) immunoglobulin-like domain and the first (of 5) extracellular fibronectin domain, respectively; 2 splice site mutations, c.1828 + 1G>A (localizing to intron 15) and c.1546 + 1G>T (located in intron 13) were associated with loss-of-function translation frameshifts; and the stop-gain mutation p.Glu304X. The previously reported deleterious missense mutation p.Val788Phe (localizing to the second fibronectin domain),5 and the known splice site mutation c.806 + 1G>C (positioned in intron 8),6 were also identified (Figure). All 6 patients for whom clinical information was available had neurodevelopmental delays. Classic L1 syndrome findings of bilateral adducted thumbs, hypotonia, cerebral palsy, epilepsy, and white-matter hypoplasia were each seen in 3 of 6 patients. Agenesis of the corpus callosum, macrocephaly, and skeletal abnormalities were seen in 4 of 6 patients.

Table.  Clinical Presentation and L1CAM Mutation Detailsa
Clinical Presentation and L1CAM Mutation Detailsa
Figure.  Transmitted and Unphased Mutations in L1CAM
Transmitted and Unphased Mutations in L1CAM

A, Available clinical neuroimaging phenotypes of congenital hydrocephalus probands with mutations in L1CAM. B, Mutation mapping of all identified L1CAM mutations. C, Pedigrees and sequencing electropherograms of Sanger sequencing depict L1CAM mutations in genomic DNA from congenital hydrocephalus probands. The mutation in proband KCHYD612-1 was not validated by Sanger sequencing owing to coronavirus disease 2019–related laboratory disruptions. Our Sanger validation rate is greater than 99%.


Detection of these probands harboring L1CAM mutations suggests caregivers are missing opportunities to obtain a genetic diagnosis in patients with CH, with potential prognostic and therapeutic implications. This could result from a failure to recognize a syndromic phenotype, from a lack of awareness of available testing, and/or from the test used being incapable of identifying novel point mutations. Although our cohort size is limited and lacks ethnic diversity, these data highlight the diagnostic utility of WES in sporadic CH in contrast to other screening strategies. Given the discovery that rare mutations with large effect, including de novo mutations, account for a significant percentage of CH cases,1 WES should be considered an essential diagnostic adjunct in the workup of all patients with sporadic perinatal CH.

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Article Information

Corresponding Author: Kristopher T. Kahle, MD, PhD, Department of Neurosurgery, Yale School of Medicine, 333 Cedar St, Tompkins 418, New Haven, CT 06520 (kristopher.kahle@yale.edu).

Accepted for Publication: April 21, 2020.

Published Online: November 16, 2020. doi:10.1001/jamapediatrics.2020.4878

Author Contributions: Dr Kahle had full access to all of the data in the study and takes responsibility for the integrity of the data and the accuracy of the data analysis. Messrs Sullivan and Reeves were equal contributors.

Concept and design: Kahle, Jin.

Acquisition, analysis, or interpretation of data: Sullivan, Reeves, Duy, Nelson-Williams, Dong, Jin.

Drafting of the manuscript: Kahle, Sullivan, Reeves.

Critical revision of the manuscript for important intellectual content: All authors.

Statistical analysis: Duy, Dong, Jin.

Obtained funding: Kahle, Jin.

Administrative, technical, or material support: Kahle, Nelson-Williams, Jin.

Supervision: Kahle, Jin.

Conflict of Interest Disclosures: None reported.

Funding/Support: Dr Kahle is supported by the Yale–National Institutes of Health Center for Mendelian Genomics (5U54HG006504); R01 NS111029-01A1, R01 NS109358, K12 228168, and the Rudi Schulte Research Institute. Dr Jin was supported by the James Hudson Brown-Alexander Brown Coxe Postdoctoral Fellowship, an American Heart Association Postdoctoral Fellowship, and the National Heart, Lung, and Blood Institute of the National Institutes of Health under award number K99HL143036 and R00HL143036-02. Messrs Reeves and Duy are supported by the National Institutes of Health Medical Scientist Training Program Training Grant T32GM136651.

Role of the Funder/Sponsor: The funding sources had no role in the design and conduct of the study; collection, management, analysis, and interpretation of the data; preparation, review, or approval of the manuscript; and decision to submit the manuscript for publication.

Additional Contributions: We thank the patients and families who participated in this research for their invaluable role in this study and the Hydrocephalus Association (HA). We thank August Allocco, BS, Yale University, and Adam J. Kundishora, MD, Yale School of Medicine, for their contribution to cohort ascertainment, recruitment, and phenotypic characterization. No compensation was received from a funding source for these contributions.

Additional Information: The sequencing data for all congenital hydrocephalus parent-offspring trios reported in this study have been deposited in the National Center for Biotechnology Information database of Genotypes and Phenotypes under the accession number phs000744.v4.p2.

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