The ClinGen Epilepsy Gene Curation Expert Panel—Bridging the divide between clinical domain knowledge and formal gene curation criteria

The field of epilepsy genetics is advancing rapidly and epilepsy is emerging as a frequent indication for diagnostic genetic testing. Within the larger ClinGen framework, the ClinGen Epilepsy Gene Curation Expert Panel is tasked with connecting two increasingly separate fields: the domain of traditional clinical epileptology, with its own established language and classification criteria, and the rapidly evolving area of diagnostic genetic testing that adheres to formal criteria for gene and variant curation. We identify critical components unique to the epilepsy gene curation effort, including: (a) precise phenotype definitions within existing disease and phenotype ontologies; (b) consideration of when epilepsy should be curated as a distinct disease entity; (c) strategies for gene selection; and (d) emerging rules for evaluating functional models for seizure disorders. Given that de novo variants play a prominent role in many of the epilepsies, sufficient genetic evidence is often awarded early in the curation process. Therefore, the emphasis of gene curation is frequently shifted toward an iterative precuration process to better capture phenotypic associations. We demonstrate that within the spectrum of neurodevelopmental disorders, gene curation for epilepsy-associated genes is feasible and suggest epilepsy-specific conventions, laying the groundwork for a curation process of all major epilepsy-associated genes

Consensus interpretation of the p.Met34Thr and p.Val37Ile variants in GJB2 by the ClinGen Hearing Loss Expert Panel

Purpose: Pathogenic variants in GJB2 are the most common cause of autosomal recessive sensorineural hearing loss. The classification of c.101T>C/p.Met34Thr and c.109G>A/p.Val37Ile in GJB2 are controversial. Therefore, an expert consensus is required for the interpretation of these two variants. Methods: The ClinGen Hearing Loss Expert Panel collected published data and shared unpublished information from contributing laboratories and clinics regarding the two variants. Functional, computational, allelic, and segregation data were also obtained. Case-control statistical analyses were performed. Results: The panel reviewed the synthesized information, and classified the p.Met34Thr and p.Val37Ile variants utilizing professional variant interpretation guidelines and professional judgment. We found that p.Met34Thr and p.Val37Ile are significantly overrepresented in hearing loss patients, compared with population controls. Individuals homozygous or compound heterozygous for p.Met34Thr or p.Val37Ile typically manifest mild to moderate hearing loss. Several other types of evidence also support pathogenic roles for these two variants. Conclusion: Resolving controversies in variant classification requires coordinated effort among a panel of international multi-institutional experts to share data, standardize classification guidelines, review evidence, and reach a consensus. We concluded that p.Met34Thr and p.Val37Ile variants in GJB2 are pathogenic for autosomal recessive nonsyndromic hearing loss with variable expressivity and incomplete penetrance

Clinical validity assessment of genes frequently tested on intellectual disability/autism sequencing panels.

[en] PURPOSE: Neurodevelopmental disorders (NDDs), such as intellectual disability (ID) and autism spectrum disorder (ASD), exhibit genetic and phenotypic heterogeneity, making them difficult to differentiate without a molecular diagnosis. The Clinical Genome Resource Intellectual Disability/Autism Gene Curation Expert Panel (GCEP) uses systematic curation to distinguish ID/ASD genes that are appropriate for clinical testing (ie, with substantial evidence supporting their relationship to disease) from those that are not. METHODS: Using the Clinical Genome Resource gene-disease validity curation framework, the ID/Autism GCEP classified genes frequently included on clinical ID/ASD testing panels as Definitive, Strong, Moderate, Limited, Disputed, Refuted, or No Known Disease Relationship. RESULTS: As of September 2021, 156 gene-disease pairs have been evaluated. Although most (75%) were determined to have definitive roles in NDDs, 22 (14%) genes evaluated had either Limited or Disputed evidence. Such genes are currently not recommended for use in clinical testing owing to the limited ability to assess the effect of identified variants. CONCLUSION: Our understanding of gene-disease relationships evolves over time; new relationships are discovered and previously-held conclusions may be questioned. Without periodic re-examination, inaccurate gene-disease claims may be perpetuated. The ID/Autism GCEP will continue to evaluate these claims to improve diagnosis and clinical care for NDDs

Expert specification of the ACMG/AMP variant interpretation guidelines for genetic hearing loss

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Spastic Paraplegia Mutation N256S in the Neuronal Microtubule Motor KIF5A Disrupts Axonal Transport in a <em>Drosophila</em> HSP Model

<div><p>Hereditary spastic paraplegias (HSPs) comprise a group of genetically heterogeneous neurodegenerative disorders characterized by spastic weakness of the lower extremities. We have generated a <em>Drosophila</em> model for HSP type 10 (SPG10), caused by mutations in KIF5A. KIF5A encodes the heavy chain of kinesin-1, a neuronal microtubule motor. Our results imply that SPG10 is not caused by haploinsufficiency but by the loss of endogenous kinesin-1 function due to a selective dominant-negative action of mutant KIF5A on kinesin-1 complexes. We have not found any evidence for an additional, more generalized toxicity of mutant Kinesin heavy chain (Khc) or the affected kinesin-1 complexes. Ectopic expression of <em>Drosophila</em> Khc carrying a human SPG10-associated mutation (N256S) is sufficient to disturb axonal transport and to induce motoneuron disease in <em>Drosophila</em>. Neurofilaments, which have been recently implicated in SPG10 disease manifestation, are absent in arthropods. Impairments in the transport of kinesin-1 cargos different from neurofilaments are thus sufficient to cause HSP–like pathological changes such as axonal swellings, altered structure and function of synapses, behavioral deficits, and increased mortality.</p> </div

ClinGen expert clinical validity curation of 164 hearing loss gene-disease pairs

Proper interpretation of genomic variants is critical to successful medical decision making based on genetic testing results. A fundamental prerequisite to accurate variant interpretation is the clear understanding of the clinical validity of gene-disease relationships. The Clinical Genome Resource (ClinGen) has developed a semiquantitative framework to assign clinical validity to gene-disease relationships. The ClinGen Hearing Loss Gene Curation Expert Panel (HL GCEP) uses this framework to perform evidence-based curations of genes present on testing panels from 17 clinical laboratories in the Genetic Testing Registry. The HL GCEP curated and reviewed 142 genes and 164 gene-disease pairs, including 105 nonsyndromic and 59 syndromic forms of hearing loss. The final outcome included 82 Definitive (50%), 12 Strong (7%), 25 Moderate (15%), 32 Limited (20%), 10 Disputed (6%), and 3 Refuted (2%) classifications. The summary of each curation is date stamped with the HL GCEP approval, is live, and will be kept up-to-date on the ClinGen website ( https://search.clinicalgenome.org/kb/gene-validity ). This gene curation approach serves to optimize the clinical sensitivity of genetic testing while reducing the rate of uncertain or ambiguous test results caused by the interrogation of genes with insufficient evidence of a disease link

Light microscopic analysis of NMJ degeneration.

<p>Degeneration was revealed and scored by immunofluorescent staining. All larvae carried one copy of the motoneuron-specific driver D42-Gal4 and were raised at 29°C. (A–D) Confocal images of immunofluorescent staining showing NMJs 6/7, segment A5 of mid-third-instar <i>Drosophila</i> larvae. To visualize the subsynaptic reticulum, we used a GFP insertion in the discs-large locus. Neuronal membranes were visualized with an antibody against horseradish peroxidase (HRP). Synaptic vesicles were stained using m-α-Synapsin (Syn) antibody. For Khc^N262S- and Khc^wt+N262S-expressing larvae, which showed a strong reduction in Syn intensity, an additional, false-colored panel (high exposure) is shown. In this panel, the brightness was adjusted for better visibility of weak signals. Scale bar: 10 µm; right panels 5 µm. Genotypes: (A) D42>w¹¹¹⁸; (B) D42>Khc^wt; (C) D42>Khc^N262S; (D) D42>Khc^wt+N262S. (E) To integrate the frequency of retractions, we used a neurodegenerative scoring system to combine the occurrence of dystrophic boutons and minor pathological alterations at the NMJs into a single measure for the degree of pathological alterations (for details see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003066#pgen.1003066.s001" target="_blank">Figure S1A</a>–<a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003066#pgen.1003066.s001" target="_blank">S1F</a>). Using this scoring system, we detected a significant degree of neurodegenerative alterations in larvae expressing Khc^N262S either alone or in combination with Khc^wt. Statistical significance was determined using a Kruskal-Wallis H-test followed by a Dunn's test for comparisons between multiple groups. The standard error of the mean (s.e.m.) is shown as a box, the standard deviation (s.d.) as a black line. ** p<0.01.</p

<i>In vivo</i> analysis of axonal transport.

<p>(A–D) Confocal analysis of mitochondrial transport in living larvae after bleaching a segment of the nerve. (A–D) Movement of mitochondria is recorded in anesthetized larvae. A representative frame of a confocal movie is shown. (A^I–D^I) Kymographs of mitochondrial transport in larvae. Mitochondria moving in anterograde and retrograde directions appear as oblique lines. Scale bar: 5 µm. (E,F) Neither anterograde nor retrograde velocity of mitochondria is significantly different between any of the examined genotypes. Both anterograde and retrograde flux of mitochondria is reduced in mutant larvae (D42>khc^N262S and D42>khc^wt+N262S) compared with controls (D42>w¹¹¹⁸ and D42>khc^wt). Statistical significance was determined using a Kruskal-Wallis H-test followed by a Dunn's test for comparisons between multiple groups. The standard error of the mean (s.e.m) is shown as a box, the standard deviation (s.d.) as a black line. * p<0.05; ** p<0.01. (See also <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003066#pgen.1003066.s010" target="_blank">Videos S4</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003066#pgen.1003066.s011" target="_blank">S5</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003066#pgen.1003066.s012" target="_blank">S6</a>, <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003066#pgen.1003066.s013" target="_blank">S7</a>).</p