16p13.11 microdeletion uncovers loss-of-function of a MYH11 missense variant in a patient with megacystis-microcolon-intestinal-hypoperistalsis syndrome.
The main results reproduced: recomputed values matched the published ones within tolerance.
Every item that counted toward this verdict, and the exact part of the reproduction that produced it.
- ✓Reported values are derivable from the shared data
- ✓Any deviation was negligible
- ✓The central claim held under reproduction
- 🟡Could not use the authors’ exact input data
- 🟡Reported values were only indirectly comparable
- 🟡A deviation arose in the data or preprocessing
- 🔴A deviation was attributed to the published material
- 🟡Overall, the reproduction showed a material discrepancy
A 0–100 reproducibility-quality score from the per-question grades, shown as a z-score: standard deviations above (+) or below (−) the mean of comparable assessments.
▸Reproduction agent’s raw note
Clinical case report (Kloth 2019, Clin Genet) of compound-heterozygous MYH11 loss in MMIHS. Two of three reported results are wet-lab (Sanger, arrayCGH) and one is clinical phenotyping -> out of scope; no patient data were deposited (no accession, no data-availability statement, paywalled). The ONLY pipeline-derived result is an in-text molecular-modeling claim about MYH11 p.Pro127Ser. We reproduced it as a third-party-tool exercise on the public MYH11 protein using the chicken smooth-muscle myosin motor-domain structure PDB 1BR2 (MgADP.AlF4-) with Biopython + PyMOL: Pro127 directly contacts the adenine of the bound nucleotide (3.5 A) and lines the ATP pocket alongside the P-loop (positive controls at 2.0-2.8 A validate the geometry), and it is invariant across 6 myosins -> claim C1 'crucial for ATP-pocket formation' is independently CONFIRMED. Modeling P127S swaps the hydrophobic ring packing on adenine for a polar Ser-OH and abolishes the proline backbone constraint -> claim C2 'alters nucleotide binding' is qualitatively SUPPORTED (not quantified; would need MD/experiment). All six standard missense predictors call P127S damaging, corroborating the loss-of-function interpretation. Overall: the paper's single computational claim is described well enough at the conclusion level to reproduce qualitatively, but the authors disclose no modeling method/template/coords, so this matches the CONCLUSION, not their exact procedure; grade partial. NOT attempted: variant detection from patient data (private/not deposited), CNV calling from arrayCGH, clinical phenotyping. This is NOT a drop (a real, gradeable in-silico reproduction was achievable) but it is honestly partial given the qualitative target and absent deposition.
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.
Assessment versions
Every reproduction run is kept as an immutable version — anchored to the data as it stood, with a tamper-evident chain hash. A rerun (e.g. after an author updates a deposit) adds a new version; the previous one stays on record.
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v1 current initial assessment Score 78assessed: 2026-06-18 ⛓ 6a34977ad3b1
✎ I am an author of this paper
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
- 2026-06-18
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-18no human curator yet
- Last updated
- 2026-08-05
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.
Scope — pmid-31044419
Paper: Kloth K, et al. 16p13.11 microdeletion uncovers loss-of-function of a MYH11 missense variant in a patient with megacystis-microcolon-intestinal- hypoperistalsis syndrome. Clin Genet. 2019. DOI 10.1111/cge.13557. PMID 31044419. (Paywalled, Wiley; no PMC, no open-access full text, no data-availability statement, no code repository, no deposited accession.)
Study type: single-patient clinical case report (trio: proband + parents).
Reported results and their nature
| # | Reported result | Method (paper) | In/out of scope | Why |
|---|---|---|---|---|
| R1 | Heterozygous missense MYH11 c.379C>T p.(Pro127Ser) in proband, paternally inherited |
Sanger sequencing (wet-lab) | OUT | Wet-lab readout; raw data not deposited (private clinical) |
| R2 | Heterozygous 1.3 Mb deletion at 16p13.11 spanning the whole MYH11 gene, maternally inherited | array CGH (wet-lab) | OUT | Wet-lab readout; raw CGH data not deposited |
| R3 | Clinical phenotype (MMIHS + GH deficiency + central hypothyroidism + tonic pupil) | clinical | OUT | Manual/clinical, not a pipeline |
| C1 | "Proline 127 is crucial for the formation of the ATP binding pocket of the MYH11 motor domain" | molecular modeling (in-silico) | IN | The only computational/pipeline-derived claim |
| C2 | "molecular modeling indicated that p.Pro127Ser alters nucleotide binding properties" | molecular modeling (in-silico) | IN | Computational claim |
Pipeline named per in-scope result
The paper does not disclose the modeling software, template structure, or parameters (abstract only; methods paywalled, no supplement available). The claim is therefore reproduced as a third-party-tool-on-the-paper's-data exercise (explicitly endorsed by the brief, P16): the paper's "data" for this claim is the public MYH11 reference protein and the location of the variant. We independently test the structural claim with:
- Template: PDB 1BR2 — chicken smooth-muscle myosin (MYH11) motor domain
crystallised with MgADP·AlF4⁻ (closest available homolog of human MYH11,
90% identity; no human MYH11 motor-domain + nucleotide structure exists).
- Tools: Biopython 1.87 (sequence→structure mapping, atom-distance geometry), PyMOL-open-source 3.1.0 (in-silico mutagenesis of Pro→Ser), a 6-myosin conservation panel, and standard missense predictors (dbNSFP via myVariant.info) as corroboration.
Explicitly NOT attempted
- Re-deriving the variant calls from patient Sanger/CGH data (no data deposited;
clinical/private — would be
data_restricted/not-deposited). - The exact modeling the authors ran (method undisclosed → cannot be byte-for-byte reproduced; we reproduce the conclusion, not their unstated procedure).
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.
This is a clinical case report whose only pipeline-derived target is a qualitative molecular-modeling claim about MYH11 p.Pro127Ser. Independent structural analysis (PDB 1BR2: Pro127 3.5 A from ADP adenine, invariant in 6/6 myosins; P127S swaps hydrophobic ring packing for a polar OH) confirms C1 and supports C2, and 6/6 missense predictors corroborate loss-of-function — the central conclusion holds (q5/q7 green, q6 negligible). The deviations are on availability/method, not the authors' computation: claims are qualitative (no 1:1 endpoint), the modeling template/coords are undisclosed (q4 red, authors' side, paper incomplete), and the wet-lab/clinical data were never deposited. Overall yellow: a solid, explainable conclusion-level reproduction, not a 1:1 match.
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.
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Reproduction footprint
claude-opus-4-8Measured resources invested to assess this paper — sanitised (machine class only, no job ids/paths). Compute = HPC accounting (SLURM); tokens = the AI agent's session.