The novel duplication HRAS c.186_206dup p.(Glu62_Arg68dup): clinical and functional aspects.
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.
- ✓Same input data as the authors
- ✓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
- ✓The central claim held under reproduction
- ✓Overall, the reproduction was clean
- Every checked point held up.
▸Reproduction agent’s raw note
DROP (non_pipeline). PMID 32499600 (Gripp et al., Eur J Hum Genet 2020; PMC7576819) is a single-patient clinical case report plus wet-lab functional characterization of the novel in-frame HRAS duplication p.(Glu62_Arg68dup). All reported results are wet-lab (transient transfection, GST pull-down/co-IP, immunoblot densitometry of MEK1/2 & ERK1/2 phosphorylation) or clinical. The only computational touch-points are Face2Gene (proprietary, closed-source, run on the patient's identifiable non-shareable facial photo) and a two-tailed t-test on densitometry that was never deposited. There is NO code repository, NO public data accession (searched GEO/SRA/ENA/ArrayExpress/dbGaP/EGA/PRIDE/PDB/figshare/Zenodo — none), NO structural modeling/molecular dynamics, and NO sequencing-analysis pipeline. Nothing is pipeline-derived and reproducible, so no «our HPC» compute was submitted. This is honest and verifiable from the open-access PMC full text. Did NOT attempt the wet-lab or proprietary-tool results because they are out of scope and have no public inputs.
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Assessment versions
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v1 current initial assessmentassessed: 2026-06-18 ⛓ 1343b00ef2b6
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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
- 2026-06-18
- Rubric version
- v1.0
- Assessed by
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🤖 AI curator · probe · 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.
Deep full-text extraction
Model: opusDoes a novel in-frame HRAS duplication variant predicting p.(Glu62_Arg68dup), identified in a patient with RASopathy features, act as an activating Costello syndrome-causing allele, and how does its altered effector/regulator interaction profile relate to clinical severity?
- ★ The novel HRAS c.186_206dup p.(Glu62_Arg68dup) variant was identified in an individual with hypertrophic cardiomyopathy, Chiari 1 malformation and ectodermal findings consistent with a RASopathy. finding
- ★ HRAS Glu62_Arg68dup alters HRAS interaction with effector PIK3CA and with the regulator neurofibromin 1 (NF1) GAP. mechanism
- ★ HRAS Glu62_Arg68dup shows enhanced binding to effectors RAF1, RALGDS and PLCE1. mechanism
- ★ p.Glu62_Arg68dup increased steady-state phosphorylation of MEK1/2 and ERK1/2 downstream of RAF1, whereas AKT phosphorylation downstream of PI3K was not significantly affected. finding
- ★ Expression of HRAS Glu62_Arg68dup abolished HRAS' capacity to modulate downstream signaling upon growth factor stimulation. finding
- ★ Different qualities of dysregulated HRAS-dependent signaling dynamics determine clinical severity in Costello syndrome. mechanism
- A clinically suspected Costello syndrome diagnosis can be confirmed through identification of a dominant pathogenic HRAS variant. method
| Assay | System | Perturbation | Readout | Platform |
|---|---|---|---|---|
| Protein-protein interaction / effector binding assay | HRAS Glu62_Arg68dup variant protein | in-frame duplication variant (p.Glu62_Arg68dup) | binding to effectors (PIK3CA, RAF1, RALGDS, PLCE1) and regulator NF1 GAP | — |
| Phosphorylation analysis (e.g. Western blot) | cells expressing HRAS Glu62_Arg68dup | expression of HRAS Glu62_Arg68dup variant | steady-state phosphorylation of MEK1/2, ERK1/2 and AKT | — |
| Growth factor stimulation signaling assay | cells expressing HRAS Glu62_Arg68dup | growth factor stimulation | modulation of downstream signaling | — |
- ▲ HRAS Glu62_Arg68dup shows enhanced binding to effectors RAF1, RALGDS and PLCE1
- ▲ Increased steady-state phosphorylation of MEK1/2 and ERK1/2 downstream of RAF1
- – AKT phosphorylation downstream of PI3K not significantly affected
- ▼ Expression of HRAS Glu62_Arg68dup abolished HRAS' capacity to modulate downstream signaling upon growth factor stimulation
- – Altered HRAS interaction with effector PIK3CA and regulator NF1 GAP
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.
The paper combines a single-patient clinical case report of a novel HRAS in-frame duplication with functional biochemical studies examining the variant's effects on protein–effector binding and downstream signaling phosphorylation. Statistical inference is implied at least for AKT phosphorylation comparisons ('not significantly affected'), though the specific tests, replication strategy, and reporting parameters are not described in the excerpt provided. The functional conclusions are drawn from binding assays and phosphorylation readouts comparing the novel variant to controls.
| Test | Applied to | n | Assumptions |
|---|---|---|---|
| Not stated (implied statistical test for phosphorylation comparisons) | AKT phosphorylation downstream of PI3K; MEK1/2 and ERK1/2 phosphorylation | — | not stated |
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Phosphorylation differences are described as 'increased' or 'not significantly affected' without reported numerical effect sizes or p-values↳ Could also: Reporting fold-change with 95% confidence intervals (e.g., from quantified densitometry normalized to loading controls) alongside explicit p-values — Numerical effect sizes and confidence intervals allow readers to assess the magnitude and precision of differences independently of a binary significant/non-significant framing, which is especially informative for small-n biochemical experiments
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Multiple phosphorylation targets (MEK1/2, ERK1/2, AKT) and multiple effector binding partners (RAF1, RALGDS, PLCE1, PIK3CA, NF1-GAP) were assessed, implying multiple comparisons↳ Could also: A family-wise or false-discovery-rate correction (e.g., Bonferroni or Benjamini–Hochberg) applied across the set of comparisons — When several endpoints are tested, multiplicity corrections reduce the probability that any one 'significant' finding is a false positive; reporting which correction was applied (or a rationale for none) aids interpretation
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The number of independent biological replicates underlying the phosphorylation and binding assays is not stated in the available text↳ Could also: Explicit statement of biological vs. technical replicates (e.g., n = 3 independent transfections) with individual data points shown alongside summary statistics — Distinguishing biological from technical replication—and displaying all data points rather than only means—allows readers to judge variability and reproducibility, which is especially important for cell-based or in-vitro assays
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Phosphorylation comparisons between variant and wild-type HRAS appear to be made at single time-points↳ Could also: Time-course experiments with repeated-measures ANOVA or mixed-effects modelling across multiple time-points — The abstract mentions that growth factor stimulation 'abolished the HRAS capacity to modulate downstream signaling dynamics', which implies a temporal dimension; explicitly modelling the time-by-genotype interaction would quantify whether and when the variant diverges from wild-type
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Binding affinity differences between HRAS variants and effectors are described qualitatively ('enhanced', 'affects')↳ Could also: Quantitative binding assays (e.g., GST pull-down densitometry, surface plasmon resonance, or biolayer interferometry) with Kd or relative enrichment values reported with standard deviations — Quantitative binding parameters allow comparison across studies and support mechanistic modelling of how the duplication alters effector selectivity
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This is a single-patient clinical case combined with functional cell assays, with no stated power calculation↳ Could also: A brief post-hoc power statement or equivalence framing for the functional assays (e.g., the study was powered to detect a fold-change of X with SD of Y at 80% power) — Even for mechanistic studies, a power or sensitivity statement helps readers understand what magnitude of difference the assay could reliably detect, which contextualises null results such as the non-significant AKT finding
What was reproduced
The exact results taken into scope, with each reported value next to the value our attempt produced.
Scope analysis — PMID 32499600
Title: The novel duplication HRAS c.186_206dup p.(Glu62_Arg68dup): clinical and functional aspects. Journal: European Journal of Human Genetics (2020). DOI 10.1038/s41431-020-0662-4. PMCID PMC7576819. Authors: Gripp KW, Baker L, Robbins KM, Stabley DL, Bellus GA, Kolbe V, Nauth T, Rosenberger G.
What kind of study is this?
A single-patient clinical case report combined with wet-lab functional characterization of a novel in-frame HRAS duplication (a RASopathy / Costello- spectrum variant). It is NOT a computational / bioinformatic-pipeline paper.
Reported results, classified by reproducibility scope
| # | Reported result | Method | In scope (pipeline-derived)? |
|---|---|---|---|
| R1 | Patient phenotype: HCM, Chiari-1 malformation, ectodermal RASopathy features; novel variant c.186_206dup / p.(Glu62_Arg68dup) | Clinical exam + Sanger/diagnostic sequencing of one patient | OUT — wet-lab/clinical, single patient, no deposited sequence data |
| R2 | Face2Gene (FDNA, v19.1.7) facial-gestalt match to a RASopathy | Proprietary closed-source deep-learning service run on the patient's private facial photograph | OUT — proprietary tool + non-shareable identifiable patient image; not reproducible |
| R3 | Enhanced binding of HRAS^Glu62_Arg68dup to RAF1, RALGDS, PLCE1; altered interaction with PIK3CA and NF1 | GST pull-down / co-immunoprecipitation in HEK293T & MCF7 | OUT — wet-lab biochemistry |
| R4 | Increased MEK1/2 and ERK1/2 phosphorylation; abolished growth-factor modulation of downstream signaling (EGF 10 ng/ml, 5/15/30 min) | Transient transfection, immunoblot, densitometry | OUT — wet-lab; quantification is densitometry of the authors' own blots |
| R5 | Significance markers (*P<0.05, two-tailed t-test) on the blot quantifications | Two-tailed t-test (software unnamed) | OUT — trivial statistics applied to non-deposited wet-lab measurements; no raw data shipped |
Pipeline-derived results in scope: NONE
There is no bioinformatic pipeline, no sequencing-data analysis, no structural modeling / molecular dynamics, no variant-effect-prediction pipeline, no code repository, and no public data accession (no GEO/SRA/ENA/PDB/Zenodo/figshare). The "Data/Code availability" of the paper deposits nothing; methods are in a Supporting-Information PDF describing wet-lab protocols only.
The only computational touch-points (Face2Gene; a two-tailed t-test) are either proprietary + dependent on a non-shareable identifiable patient photo (R2), or trivial statistics on wet-lab measurements that were never deposited (R5). Neither is a reproducible pipeline-derived result with a public input.
Decision
DROP — drop_reason = non_pipeline (with no_data_accession + no_code as
secondary evidence). No heavy compute submitted to «our HPC»: there is nothing to
run. This conclusion is honest and verifiable from the open-access PMC full text.
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.
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
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