Hereditary parkinsonism with dementia is caused by mutations in ATP13A2, encoding a lysosomal type 5 P-type ATPase.
Part of the results reproduced; minor but material deviations remained.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓No authors-side cause for any deviation
- ✓Any deviation was negligible
- 🔴Could not use the authors’ exact input data
- 🔴Reported values were only indirectly comparable
- 🟡A deviation arose in the data or preprocessing
- 🟡Reported values were not (fully) derivable from the shared data
- 🟡The central claim did not (fully) hold under reproduction
- 🟡Overall, the reproduction showed a material discrepancy
This paper has a computational component, but its primary data is legally or ethically access-restricted — identifiable patient cohorts, rare-disease genomes, or controlled-access biobanks that cannot be openly shared. The reproduction therefore could not be attempted. That is a neutral verdict: it does not mean the result is wrong or that the authors fell short — only that, for legitimate privacy reasons, it cannot be independently checked from public data. We deliberately do NOT assign a 0–100 score here, because a low number would wrongly read as a failed reproduction.
▸Reproduction agent’s raw note
DROP. This is a 2006 Nature Genetics discovery paper (Ramirez et al., PMID 16964263) reporting ATP13A2 loss-of-function mutations as the cause of Kufor-Rakeb syndrome (PARK9), found via family linkage/homozygosity mapping (1p36 interval, previously established in a 2001 J Med Genet paper) plus Sanger-sequencing-based candidate-gene screening, RT-PCR expression, and cell-biology assays. The article is paywalled with no PMC/open-access copy (confirmed via Europe PMC: isOpenAccess=N, inEPMC=N, subscription required, no PMCID) and no code or data repository is listed. Independent of the paywall, a targeted search (Europe PMC + NCBI E-utilities elink to nuccore/nuccore_refseq/clinvar) found no primary dataset (raw genotypes, sequencing traces, expression data) deposited by the authors anywhere public — only downstream ClinVar citation records and generic ATP13A2 reference-sequence records, neither of which constitutes rerunnable pipeline input. All of the paper's reported results are wet-lab/manual genetics analysis from the pre-NGS era rather than an independently rerunnable bioinformatic pipeline with accessible inputs, so nothing in-scope could be attempted. A «our HPC»/SLURM connectivity smoke test («job», ran on compute node n114) confirmed the HPC path itself is functional, ruling out an infrastructure-side reason for the drop — this is a genuine, well-founded drop (paywall + no deposited primary data), not a failure of our compute access.
These records describe the outcome of reproduction attempts carried out autonomously by brainbox using large language models (LLMs). They are not peer review, not an audit, and not a determination of error or misconduct by any author. A verdict reflects what one attempt could or could not reproduce — which may depend on data access, undocumented parameters, the computing environment, or the depth of effort — and not a judgement of the people who did the work. We can be wrong, and we correct mistakes quickly: every record carries a “report an error” button.
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Updated or fixed a deposit, or is there an erratum? Ask us to re-run the metrics. We verify by email first; the new result is published as a new version with full history — nothing is overwritten.
Provenance — full disclosure
When this reproduction was carried out, which methodology version was used, and by whom — so the record can be audited and checked independently.
- Reproduced
- 2026-07-28
- Rubric version
- v1.0
- Assessed by
-
🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-07-31no human curator yet
- Last updated
- 2026-07-31
Provisional, curator- or AI-assessed, and independently checkable. A reproduction outcome states what one attempt could reproduce — not a judgement of the authors.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
No individual results have been recorded for this entry yet.
Assessments & scoring basis
Each contributor’s verdict, the per-question basis, and the auditable, itemised worksheet behind it.
An automated assessment. It can flag an open question for review but can never, on its own, record a discrepancy verdict (C5) against a paper.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
No reproduction was possible and none was attempted: the 2006 Nature Genetics article is paywalled (Europe PMC isOpenAccess=N, inEPMC=N, no PMCID, subscription-required DOI link), lists no code or data repository, and targeted searches (Europe PMC + NCBI elink to nuccore/nuccore_refseq/clinvar) found no deposited primary data — only ~54 downstream ClinVar records citing this PMID and generic ATP13A2 RefSeq entries. Independent of the paywall, the science itself is wet-lab/manual (microsatellite LOD-score linkage and homozygosity mapping in a Jordanian kindred, Sanger candidate-gene screening yielding a 22-bp duplication and a compound-heterozygous 1-bp deletion + splice-site mutation in a Chilean family, RT-PCR, transfection assays), so there is no rerunnable pipeline. The failure sits on the data-availability/era side, not on the authors' scientific side and not on ours — a «our HPC»/SLURM smoke test («job», node n114, completed) confirms infrastructure was fine. Accordingly q1/q2 are red (no comparable input or endpoint) while q5/q7/q8 stay yellow: the ATP13A2–PARK9 claim is unverified by us, not contradicted, and the widespread subsequent ClinVar curation of ATP13A2 variants is external corroboration that argues against any fabrication suspicion.
Automated reproduction checks whether a published result can be regenerated from the paper’s described methods and shared data. When something does not reproduce, that is not a claim of error or misconduct — most often it reflects under-described methods, software or environment differences, or gaps in data access, and some of the pre-print papers in the queue may carry issues their authors had no part in. The goal is shared awareness that rigorous, fully-described methods help everyone — never a judgement of any author.
Are you an author? We would genuinely like to hear from you — to clarify the record, add data or code, re-run the pipeline after an accession update, and publish your response right next to the assessment. Everything here is open and auditable.
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