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Mendelian error

A pedigree-genotype incompatibility where a child's called genotype is impossible from recorded parents under a stated Mendelian transmission model, used as a bounded quality-control flag.

Version
v1 · 2026-09-28 · History
Domain-specific #
10671
Domain group
Natural Sciences
Origin domain
Biology & Ecology
Subdomains
Genetics, Pedigree and Genotype Quality Control → Biology & Ecology

Core Idea

Mendelian checking compares child and parental genotype calls against possible transmissions at the same locus. An impossible combination indicates that some element of genotype, sample, pedigree, variant representation, ploidy, or biological model needs review.

It does not identify the cause by itself. Technical artifacts are common, while validated de novo variants, mosaicism, copy-number changes, and complex regions require specialized interpretation. Relationship inferences carry sensitivity and privacy obligations.

Structural Signature

Sig role-phrases:

  • Family relationship — Declares child and putative biological parents. It is pedigree. Counterfactual: Wrong or incomplete relationships alter expected transmission.
  • Genotype calls — Supply alleles at the same locus for each person. It is evidence. Counterfactual: Low-quality or mismapped calls can create false errors.
  • Inheritance model — States ploidy, chromosome, sex, and Mendelian transmission assumptions. It is rule. Counterfactual: Autosomal diploid logic cannot be applied everywhere.
  • Compatibility check — Enumerates offspring genotypes possible from parental alleles. It is operation. Counterfactual: Population rarity is not transmission impossibility.
  • Quality context — Includes depth, balance, contamination, and sample identity. It is validation. Counterfactual: A hard call can conceal uncertainty.
  • Alternative biology — Allows de novo mutation, mosaicism, structural variation, and complex loci. It is explanation. Counterfactual: Incompatibility does not automatically establish pedigree error.

What It Is Not

  • It is not a rare inherited allele.
  • It is not proof of nonparentage.
  • It is not phenotype mismatch.
  • It is not valid without locus-specific inheritance assumptions.
  • Closest near-miss. A de novo variant is biologically new in the child; it first appears as an incompatibility but requires validation and exclusion of technical and pedigree explanations.

Scope of Application

  • Genotyping QC. Detects calling and sample problems.
  • Pedigree validation. Finds relationship inconsistencies at aggregate scale.
  • De novo studies. Nominates variants for rigorous confirmation.
  • Variant pipelines. Tests representation, ploidy, and complex regions.
  • Population research. Uses aggregate rates under ethical governance.

Clarity

Record genome build, locus and alleles, variant representation, family IDs, stated relationships, sex and ploidy model, genotype likelihoods, depth, allele balance, contamination, sample identity, replicate confirmation, and alternative explanations. Protect sensitive pedigree information.

Manages Complexity

The flag compresses a family transmission constraint into an auditable incompatibility. It is valuable precisely because it postpones causal attribution until technical and biological possibilities are investigated.

Abstract Reasoning

  1. Harmonize samples, loci, alleles, and genome representation.
  2. Select the correct chromosome and ploidy inheritance model.
  3. Enumerate compatible offspring genotypes.
  4. Flag calls outside that set with uncertainty retained.
  5. Review read, sample, pedigree, and complex-locus evidence.
  6. Classify a cause only after independent confirmation.

Knowledge Transfer

The transferable cargo is constraint-based consistency checking across related records. It transfers to other pedigrees and inheritance systems when ploidy and rules are redefined; human pedigree conclusions do not travel automatically.

Examples

Applied / In Practice

Two high-confidence homozygous reference parents and a heterozygous child call create an incompatibility under simple diploid transmission, triggering review.

Mapped back: model → autosomal diploid; status → flag.

Applied / In Practice

Read review reveals allele dropout in one parent; corrected genotype restores compatibility.

Mapped back: cause → calling error.

Applied / In Practice

A child inherits one rare allele from a heterozygous parent; rarity is not a Mendelian error.

Mapped back: transmission → possible.

Structural Tensions

T1 — Qc Sensitivity versus False Flags. Strict checks detect sample and calling problems but complex loci violate simple assumptions.

Diagnostic: Is this locus model valid?

T2 — Pedigree Signal versus Privacy And Uncertainty. Clusters may suggest relationship issues but single sites do not prove them.

Diagnostic: What corroboration and governance apply?

T3 — Hard Calls versus Probabilistic Evidence. Thresholded genotypes simplify checks while discarding uncertainty.

Diagnostic: Would genotype likelihoods change the result?

Structural–Framed Character

Mendelian Error is hybrid: structurally a rule violation and framed by genomics, pedigree records, measurement uncertainty, alternative biology, and privacy.

Structural Core vs. Domain Accent

The core compares observed family states with allowed transmissions. Genetics adds alleles, ploidy, chromosomes, genotype likelihoods, de novo mutation, mosaicism, structural variants, sample swaps, and relationship inference.

  • Approved root. No reviewed node entails this family-genotype incompatibility class.

  • Related — Mendelian inheritance, pedigree, genotype error, de novo mutation, allele dropout, sample contamination, and kinship. These are rule, causes, or uses.

Neighborhood in Abstraction Space

Mendelian error sits in a crowded region of the domain-specific corpus (38th percentile for distinctiveness): several abstractions share nearly its structure, so a description that fits it tends to fit its neighbors too.

Family — Cellular & Evolutionary Biological Processes (16 abstractions)

Nearest neighbors

Computed from structural-signature embeddings · 2026-10-08

Not to Be Confused With

  • De Novo Mutation. Tell: One possible validated biological explanation for an apparent incompatibility.
  • Nonpaternity. Tell: A sensitive relationship hypothesis requiring genome-wide corroboration and governance.
  • Genotyping Error. Tell: A common technical cause, not the definition of the flag.
  • Hardy–Weinberg Disequilibrium. Tell: A population-level frequency departure rather than family transmission impossibility.

References

  • Frozen Wikipedia discovery revision: https://en.wikipedia.org/wiki/Mendelian_error (revision 1346161178).
  • Preserved source candidate: http://www.inra.fr/mia/T/degivry/Schiex05a.pdf
  • Preserved source candidate: https://www.pnas.org/doi/full/10.1073/pnas.0607426104
  • Preserved source candidate: http://bioinf.wehi.edu.au/folders/melanie/statgenhowto.html

The frozen Wikipedia revision is discovery provenance. The retained source set was reviewed for identity, formal or operational relation, and scope. The encyclopedia's structural synthesis is bounded to those claims; a thin authority surface is recorded as a nonblocking source-strengthening repair rather than concealed.