{"doi":"10.1002/acn3.52127","title":"Expert panel curation of 31 genes in relation to limb girdle muscular dystrophy","abstract":"OBJECTIVE: Limb girdle muscular dystrophies (LGMDs) are a group of genetically heterogeneous autosomal conditions with some degree of phenotypic homogeneity. LGMD is defined as having onset >2 years of age with progressive proximal weakness, elevated serum creatine kinase levels and dystrophic features on muscle biopsy. Advances in massively parallel sequencing have led to a surge in genes linked to LGMD. METHODS: The ClinGen Muscular Dystrophies and Myopathies gene curation expert panel (MDM GCEP, formerly Limb Girdle Muscular Dystrophy GCEP) convened to evaluate the strength of evidence supporting gene-disease relationships (GDR) using the ClinGen gene-disease clinical validity framework to evaluate 31 genes implicated in LGMD. RESULTS: The GDR was exclusively LGMD for 17 genes, whereas an additional 14 genes were related to a broader phenotype encompassing congenital weakness. Four genes (CAPN3, COL6A1, COL6A2, and COL6A3) were split into two separate disease entities, based on each displaying both dominant and recessive inheritance patterns, resulting in curation of 35 GDRs. Of these, 30 (86%) were classified as definitive, 4 (11%) as moderate, and 1 (3%) as limited. Two genes, POMGNT1 and DAG1, though definitively related to myopathy, currently have insufficient evidence to support a relationship specifically with LGMD. INTERPRETATION: The expert-reviewed assertions on the clinical validity of genes implicated in LGMDs form an invaluable resource for clinicians and molecular geneticists. We encourage the global neuromuscular community to publish case-level data that help clarify disputed or novel LGMD associations.","journal":"Annals of Clinical and Translational Neurology","year":2024,"id":466279,"datarank":0.2515659090973748,"base_score":1.6094379124341003,"endowment":1.6094379124341003,"self_citation_contribution":0.24141568686511508,"citation_network_contribution":0.010150222232259708,"self_endowment_contribution":0.24141568686511508,"citer_contribution":0.010150222232259708,"corpus_percentile":40.30324127794538,"corpus_rank":7718,"citation_count":4,"citer_count":1,"citers_with_citation_signal":1,"citers_with_endowment":1,"datacite_reuse_total":0,"is_dataset":true,"is_dataset_confidence":0.6188,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":41.6667,"fair_percentile":54.173035768878016,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":275119,"name":"Shannon McNulty","orcid":"0000-0002-0566-4629","position":1,"is_corresponding":false},{"id":95764,"name":"Courtney L Thaxton","orcid":"0000-0002-6733-369X","position":2,"is_corresponding":false},{"id":1071087,"name":"Marwa Elnagheeb","orcid":null,"position":3,"is_corresponding":false},{"id":1071089,"name":"Emma Owens","orcid":null,"position":4,"is_corresponding":false},{"id":1093799,"name":"May Flowers","orcid":null,"position":5,"is_corresponding":false},{"id":1298467,"name":"Teagan Nunnery","orcid":null,"position":6,"is_corresponding":false},{"id":1298468,"name":"Autumn Self","orcid":null,"position":7,"is_corresponding":false},{"id":1071090,"name":"Brooke Palus","orcid":null,"position":8,"is_corresponding":false},{"id":901005,"name":"Svetlana Gorokhova","orcid":"0000-0001-6870-4061","position":9,"is_corresponding":false},{"id":314503,"name":"April Kennedy","orcid":"0009-0001-3873-3168","position":10,"is_corresponding":false},{"id":869875,"name":"Zhiyv Niu","orcid":"0000-0001-6068-5505","position":11,"is_corresponding":false},{"id":1136666,"name":"Mridul Johari","orcid":"0000-0002-3549-558X","position":12,"is_corresponding":false},{"id":761924,"name":"Alassane Baneye Maīga","orcid":"0000-0002-7296-7785","position":13,"is_corresponding":false},{"id":1298469,"name":"Kelly Macalalad","orcid":null,"position":14,"is_corresponding":false},{"id":894008,"name":"Amanda Clause","orcid":"0000-0002-2078-7280","position":15,"is_corresponding":false},{"id":22060,"name":"J. Beckmann","orcid":"0000-0002-9741-1900","position":16,"is_corresponding":false},{"id":553146,"name":"Lucas Bronicki","orcid":null,"position":17,"is_corresponding":false},{"id":420737,"name":"Sandra T. Cooper","orcid":"0000-0002-7314-5097","position":18,"is_corresponding":false},{"id":1176996,"name":"Vijay S Ganesh","orcid":"0000-0002-8709-9351","position":19,"is_corresponding":false},{"id":341894,"name":"Peter B. Kang","orcid":"0000-0002-4270-7325","position":20,"is_corresponding":false},{"id":593667,"name":"Akanchha Kesari","orcid":"0000-0003-4201-901X","position":21,"is_corresponding":false},{"id":998,"name":"Monkol Lek","orcid":"0000-0003-1227-6293","position":22,"is_corresponding":false},{"id":562452,"name":"Jennifer Lévy","orcid":null,"position":23,"is_corresponding":false},{"id":759645,"name":"Laura Rufibach","orcid":"0000-0001-8208-0574","position":24,"is_corresponding":false},{"id":1136663,"name":"Marco Savarese","orcid":"0000-0002-2591-244X","position":25,"is_corresponding":false},{"id":252015,"name":"Melissa J. Spencer","orcid":"0000-0001-7104-544X","position":26,"is_corresponding":false},{"id":333621,"name":"Volker Straub","orcid":"0000-0001-9046-3540","position":27,"is_corresponding":false},{"id":982379,"name":"Giorgio Tasca","orcid":"0000-0003-0849-9144","position":28,"is_corresponding":false},{"id":420105,"name":"Conrad C. Weihl","orcid":"0000-0002-3816-6124","position":29,"is_corresponding":false},{"id":482869,"name":"Shruthi Mohan","orcid":"0000-0002-2796-282X","position":0,"is_corresponding":true}],"reference_count":31,"raw_metadata":null,"created_at":"2026-07-19T02:04:54.606394Z","pmid":"39215466","pmcid":"PMC11537137","fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":50.0,"fair_a":62.5,"fair_i":20.0,"fair_r":16.6667,"fair_zscore":0.2857,"fair_rationale":{"fair_score":41.67,"has_llm":true,"taxonomy_version":"fair_taxonomy_v5","dimensions":{"F":{"name":"Findable","score":50.0,"criteria":[{"key":"f_dataset_pid","label":"Persistent identifier for the data","kind":"llm","weight":2.0,"fraction":0.5,"verdict":"partial","evidence":"The data described in this manuscript are available through the ClinGen website 12 and from the corresponding author via request.","grounded":true,"rationale":"The strongest identifier given is a web URL (https://search.clinicalgenome.org/...), not a persistent identifier scheme. 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It is the cheapest single thing that makes a dataset usable by someone who was not in the lab, and a table buried in the article does not travel with the data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"Table 1. Clinical validity classification of curated gene–disease relationships.","why":"Variable-level definitions (gene list, classifications) are provided inside the article via Table 1, but no documentation object is stated to accompany the data in the repository. [downgraded to 'no' — no verifiable quote from the paper]","gain":0.0,"priority":"important","scored":false},{"key":"a_controlled_access_for_sensitive","dimension":"A","label":"Gatekeeper for sensitive data","action":"Route sensitive data through an institutional gatekeeper — deposit in a controlled- access repository (dbGaP, EGA) with a Data Access Committee and a published DUA — rather than through the corresponding author's inbox. An author-gated dataset dies with the author's email address, and 'on reasonable request' has been shown repeatedly not to yield data.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"The data are not sensitive human-subject data, and no gatekeeper of any kind is named; the criterion is not applicable and no artefact exists.","gain":0.0,"priority":"useful","scored":false},{"key":"i_qualified_references","dimension":"I","label":"Identifiers for the resources the data depend on","action":"Cite by identifier every resource the data depend on — the source datasets' accessions, the reference build (GRCh38 / GCA_000001405.28), the cohort application number, the code DOI — and register those relations on the dataset record (IsDerivedFrom, IsSupplementTo). A name is not a link: it cannot be resolved, versioned, or followed by a machine.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":"https://search.clinicalgenome.org/kb/affiliate/10061?page=1&size=25&search=","why":"The paper provides a URL identifier for the ClinGen curation page, an external resource. [downgraded to 'no' — no verifiable quote from the paper] [majority verdict 'no' (4/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false},{"key":"a_timeline_retention","dimension":"A","label":"Availability timing & retention","action":"State when the data become available AND how long they will be retained — cite the repository's preservation policy. NIH DMS Element 4 asks for both; most papers give neither.","anchors":["yes","partial","no"],"verdict":"no","current":0.0,"evidence":null,"why":"No sentence in the paper addresses the timing or persistence of the data's availability. [majority verdict 'no' (3/5 passes agreed)]","gain":0.0,"priority":"useful","scored":false}],"suggestions":["Attach a standard, machine-readable open licence to the deposit — CC0 or CC BY, which is what Horizon Europe and most funders expect — and print the licence identifier in the paper. 'Free to use' is not a licence: it grants nothing a reuser's institution can rely on.","Mint or cite a persistent identifier for the dataset — a repository DOI or an accession from a registered repository — and print it in the paper. A bare URL is not persistent: it is the single most common cause of a dead data link five years after publication. For neuroimaging data, deposit in OpenNeuro or NeuroVault.","Deposit the data in a repository registered in re3data/FAIRsharing (a domain repository such as GEO, SRA, dbGaP, PRIDE, or a generalist such as Zenodo, Dryad, Dataverse) and name it explicitly in the paper. A lab website is not an archive: it has no retention commitment and no accession. For neuroimaging data, deposit in OpenNeuro or NeuroVault.","Release the data in an open, community-standard format (CSV/TSV, JSON, HDF5, NetCDF, FASTQ, VCF, NIfTI…) instead of — or alongside — any proprietary or instrument-native format, and name the format in the paper. A dataset that needs a €2,000 licence to open is not reusable. Prefer open neuroimaging formats such as NIfTI or BIDS.","Publish the analysis code in a public forge, archive a tagged release with a DOI (Zenodo/Software Heritage), and cite that DOI in the paper. NIH DMS Element 2 asks for the tools and code, not only the data — and 'available on request' is not a locator. Archive the analysis code in a versioned repository (GitHub + a Zenodo release DOI)."],"model":"deepseek/deepseek-v4-flash","agent_version":"fair_agent_v8","fulltext_source":"unpaywall_pdf"},"fair_model":"deepseek/deepseek-v4-flash","fair_agent_version":"fair_agent_v8","fair_fulltext_source":"unpaywall_pdf","fair_has_llm":true,"fair_computed_at":"2026-07-20T13:07:56.839558Z","clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}