Mutations of the mitochondrial holocytochrome c-type synthase in X-linked dominant microphthalmia with linear skin defects 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 were directly comparable
- ✓No relevant deviation in data/preprocessing
- ✓No authors-side cause for any deviation
- ✓Reported values are derivable from the shared data
- ✓Any deviation was negligible
- ✓Overall, the reproduction was clean
- 🟡Could not use the authors’ exact input data
- 🟡The central claim did not (fully) hold under reproduction
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
Wimplinger 2006 (Am J Hum Genet 79:878-889) is a classic wet-lab mutation-discovery paper (HCCS mutations in MLS/MIDAS): Sanger sequencing, Southern blot, qPCR, yeast complementation, immunofluorescence. It is fundamentally NON-PIPELINE and deposits no dataset and no code, so 6/7 reported results are out of scope. The single pipeline-derived computational claim is the Fig 3E statement that HCCS arginine-217 is invariant across heme-lyase orthologues. This was reproduced 1:1 on «our HPC»: 12 orthologue proteins (the same 12 Fig 3E species) fetched from NCBI, aligned with two independent tools (MAFFT L-INS-i and Clustal Omega), and the human-R217 alignment column is an invariant arginine in 12/12 species (0 gaps) under both tools. Verdict: partial reproduction — the one in-scope computational claim reproduced exactly; the remainder is wet-lab and not attempted. No fabrication signals (human R217 and R197 residues also confirmed in the reference protein).
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 75assessed: 2026-06-19 ⛓ c71149645dd5
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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
- 2026-06-19
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · claude (ai-curator room) · v1.0 · run #1 2026-06-19no 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.
Deep full-text extraction
Model: opusBecause microphthalmia with linear skin defects syndrome (MLS/MIDAS) maps to Xp22 and is usually caused by segmental monosomy of this region, the authors test whether point mutations or submicroscopic deletions in the HCCS gene (encoding mitochondrial holocytochrome c–type synthase) cause MLS in patients with normal karyotypes, and whether disturbed cytochrome c–dependent OXPHOS and apoptosis underlie the phenotype.
- ★ Heterozygous de novo point mutations in HCCS (missense p.R217C and nonsense p.R197X) cause X-linked dominant MLS in females with normal karyotypes finding
- ★ An 8.6-kb submicroscopic deletion encompassing part of HCCS segregates with MLS in a third family showing phenotypic variability finding
- ★ Mutant HCCS proteins R217C and Δ197–268 fail to complement a S. cerevisiae cyc3 mutant, whereas wild-type HCCS does, indicating loss of heme lyase function finding
- ★ Wild-type and R217C HCCS are targeted to mitochondria in CHO-K1 cells, but the C-terminal–truncated Δ197–268 mutant fails to be sorted to mitochondria mechanism
- HCCS functions as a heme lyase that covalently adds the prosthetic heme group to apocytochrome c and c1 mechanism
- Inability of HCCS-deficient cells to undergo cytochrome c–mediated apoptosis may shift cell death toward necrosis, causing tissue deterioration mechanism
- Disturbance of OXPHOS, the apoptosis/necrosis balance, and the X-inactivation pattern may contribute to the variable MLS phenotype mechanism
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Mutation analysis / DNA sequencing | Human patients with MLS (two families, normal karyotype) | none | HCCS point mutations (p.R217C, p.R197X) | — |
| Deletion/copy-number mapping | Human family (mother and two daughters with MLS) | none | 8.6-kb submicroscopic deletion encompassing part of HCCS | — |
| Yeast functional complementation | Saccharomyces cerevisiae mutant deficient for HCCS orthologue Cyc3p | OE (expression of wild-type or mutant HCCS: R217C, Δ197–268) | Ability to complement cyc3 deficiency | — |
| Subcellular localization / ectopic expression | CHO-K1 cells | OE (wild-type, R217C, Δ197–268 HCCS) | Mitochondrial targeting/sorting of HCCS protein | — |
- – De novo missense p.R217C and nonsense p.R197X mutations identified in HCCS in two MLS patients
- – 8.6-kb deletion encompassing part of HCCS carried by affected mother and two daughters 8.6 kb
- ▼ R217C and Δ197–268 mutants failed to complement yeast cyc3 mutant, unlike wild-type HCCS
- – Δ197–268 truncated mutant failed mitochondrial sorting, whereas wild-type and R217C were targeted to mitochondria
- other 8.6-kb deletion (Submicroscopic deletion encompassing part of HCCS in mother and two daughters of third family)
- count two female patients from two families (MLS patients with normal karyotype carrying HCCS point mutations)
Statistical methods review
Model: sonnetA neutral, descriptive read of the statistical approach — what was done, and (for shared learning, not as criticism) what could also have been done.
This is a genetics case-series/functional-study report: heterozygous de novo point mutations in HCCS were identified in two unrelated female patients with MLS syndrome, and a third family was found to carry a submicroscopic deletion spanning part of HCCS. Functional consequences of the mutant proteins were assessed with a yeast (Saccharomyces cerevisiae) complementation assay and with subcellular localization in CHO-K1 cells. The available text (title, author/affiliation metadata, and abstract) does not describe a quantitative statistical testing framework, sample sizes for the functional assays, or a formal statistical results section.
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Functional complementation of the yeast cyc3 mutant by wild-type vs. mutant HCCS was described qualitatively (able/unable to complement).↳ Could also: Quantitative scoring of complementation (e.g., colony/growth-rate counts on selective vs. non-selective media analyzed with a t-test, Mann-Whitney U, or chi-square test across replicate platings) — A quantitative statistical comparison would let readers gauge the magnitude and significance of the growth/complementation difference rather than only a binary outcome, which can be useful when differences are partial rather than absolute.
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Mitochondrial targeting of wild-type vs. mutant HCCS in CHO-K1 cells was assessed, apparently by microscopy/imaging.↳ Could also: Blinded, quantitative co-localization analysis (e.g., Pearson's or Manders' co-localization coefficients with mitochondrial markers) across a defined number of independent replicates, summarized with a dispersion measure and formal statistical comparison — Quantitative co-localization metrics with replicate-based statistics can complement representative-image reporting by providing an effect size and variability estimate for the mislocalization phenotype.
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Genotype-phenotype findings are presented as three individual families/case reports without a pooled statistical analysis.↳ Could also: A structured genotype-phenotype correlation analysis (e.g., comparing deletion/truncation extent or predicted protein consequence against phenotype severity across a larger assembled cohort, possibly with a proportional-odds or rank-based test) — As additional cases accumulate, a cohort-level statistical correlation can help formally characterize genotype-phenotype relationships, complementing descriptive case reporting, which is a standard and appropriate approach for initial rare-variant discovery of this kind.
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X-inactivation pattern is discussed as a contributor to phenotypic variability among affected females.↳ Could also: Quantitative X-inactivation skewing assays (e.g., HUMARA or methylation-sensitive assay) with statistical comparison of skewing ratios between more- and less-severely affected individuals — Quantifying and statistically comparing X-inactivation skewing across patients would provide direct, testable support for the proposed link between X-inactivation and phenotypic variability.
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope — pmid-17033964
Paper: Wimplinger I, et al. "Mutations of the mitochondrial holocytochrome c-type synthase in X-linked dominant microphthalmia with linear skin defects syndrome." Am J Hum Genet 2006;79(5):878-889. PMCID: PMC1698567.
Nature of the paper
Classic candidate-gene mutation-discovery + wet-lab functional study. Three MLS/MIDAS families. Findings: two de-novo point mutations in HCCS (p.R217C missense, p.R197X nonsense) in two sporadic female patients, and an 8.6-kb submicroscopic deletion removing HCCS exons 1-3 segregating in a third family. Functional validation by yeast (S. cerevisiae cyc3Δ) complementation and CHO-K1 subcellular localization.
Result-by-result scope classification
| # | Reported result | Method | Scope |
|---|---|---|---|
| R1 | p.R217C and p.R197X point mutations identified | Sanger sequencing of HCCS exons | OUT — wet-lab Sanger, no deposited reads/traces |
| R2 | 8.6-kb deletion of HCCS exons 1-3 | Southern blot + long-range PCR + breakpoint sequencing | OUT — wet-lab |
| R3 | Copy-number: exons 1-3 haploid in carriers (Fig 2B) | Real-time qPCR, ddCt method (Primer Express) | OUT — wet-lab assay; raw Ct values not deposited |
| R4 | Skewed X-inactivation 85-100% (Fig 6) | Methylation-specific PCR at AR locus (GENESCAN sizing) | OUT — wet-lab assay |
| R5 | Mutant proteins fail to complement yeast cyc3Δ | Yeast growth complementation | OUT — wet-lab |
| R6 | Mutant proteins mislocalize (Fig 5) | Immunofluorescence microscopy | OUT — wet-lab |
| R7 | "Arginine-217 is an invariant amino acid in all HCCS proteins" (Fig 3E) | Multiple sequence alignment of heme-lyase orthologues from 12 species | IN — computational; reproducible with a standard MSA tool on public reference protein sequences |
In-scope target (the only pipeline-derived computational claim)
R7 — conservation of R217. The paper aligns heme-lyase / HCCS orthologue proteins from Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Pan troglodytes, Macaca mulatta, Bos taurus, Candida albicans, Saccharomyces cerevisiae (Cyc3p), Schizosaccharomyces pombe, Neurospora crassa, Caenorhabditis elegans (Fig 3E) and reports that the arginine equivalent to human HCCS R217 (human HCCS = 268 aa, NP_005324) is invariant.
Reproduction strategy (BRIEF P16 third-party-tool clause): fetch the orthologue protein sequences from public NCBI RefSeq, run a standard MSA tool (MAFFT / Clustal Omega) on «our HPC», locate the alignment column carrying human HCCS R217, and check whether that column is an invariant arginine across the orthologue set. Grade = exact if R217 column is invariant Arg; partial if some divergent orthologues cannot be confidently aligned at that column.
Datasets
The paper deposits no high-throughput dataset and no code. The GenBank IDs
it cites (CR749578 cDNA clone; NM_005333 / NM_006413 RefSeq mRNAs) are reference
sequences, not study data. Profiled accordingly in data/dataset_profile.json.
Honest overall assessment
~6 of 7 reported results are wet-lab and out of scope by the study's own definition (pipeline-derived only). One small computational claim (R7, R217 conservation) is in scope and is attempted. This paper is fundamentally a non-pipeline publication; the R7 reproduction is the maximal honest computational reproduction available.
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.
Wimplinger 2006 (Am J Hum Genet 79:878-889) is a fundamentally non-pipeline wet-lab mutation-discovery paper, but unlike a pure drop it contains one in-scope computational claim (Fig 3E: HCCS arginine-217 invariant across orthologues) which was reproduced 1:1 exactly on «our HPC» — invariant R in 12/12 species, 0 gaps, identical under MAFFT and Clustal Omega, with no fabrication signal. q1 is yellow because the orthologue set was self-assembled from public sequences (the authors deposited no alignment), and q7 is yellow because the central disease-causation thesis is wet-lab and untestable here. Overall this is a clean, high-quality partial reproduction: everything computationally checkable matched exactly.
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.