Ectopic tissue: genes and variants

Genes linked to Ectopic tissue

• DCX: Neuronal migration protein doublecortin

  It stabilizes microtubules in migrating neurons and is required for orderly cortical layering during brain development. Loss-of-function variants cause X-linked lissencephaly in males and subcortical band heterotopia in many heterozygous females.

  25 disease-causing and 6 uncertain variants in DCX are linked to Ectopic tissue.

Weakly linked (only a few uncertain records): PIK3CA.

Where Ectopic tissue variants cluster

• DCX Doublecortin 2 (positions 180–263): 22 of 25 disease-causing changes, 3.8× more than its size predicts.

Known disease-causing variants in Ectopic tissue

Which prediction tools work for Ectopic tissue

How often each tool ranks a disease-causing variant above a harmless one (AUROC × 100).

• SIFT: 98 out of 100
• CATVariant: 86 out of 100 (learned from overlapping clinical labels, so this is optimistic)

Same protein, different disease

• Lissencephaly type 1 due to doublecortin gene mutation is also caused by DCX variants; they fall mostly in different places as the Ectopic tissue variants (23 disease-causing).
• Subcortical laminar heterotopia, X-linked is also caused by DCX variants; they fall mostly in different places as the Ectopic tissue variants (4 disease-causing).

Diseases related to Ectopic tissue

• Lissencephaly type 1 due to doublecortin gene mutation, also linked to DCX

Frequently asked questions

Which genes are linked to Ectopic tissue?

In CATVariant, Ectopic tissue is linked to 1 analyzed protein: DCX (Neuronal migration protein doublecortin).

How many genetic variants are linked to Ectopic tissue?

32 variants: 25 are classified as disease-causing (pathogenic or likely pathogenic) in ClinVar and 7 are of uncertain significance or have conflicting reports.

Which uncertain variants in Ectopic tissue look disease-causing?

None of the uncertain variants currently reaches the likely-pathogenic range on computable evidence alone.

Which variant effect predictor works best for Ectopic tissue?

Among tools not trained on clinical labels, SIFT separates this disease's known disease-causing variants from harmless ones best (AUROC 0.98, based on 25 disease-causing and 9 harmless variants).

About this data

Variant–disease links come from ClinVar, Open Targets and UniProt, pooled from the latest public CATVariant analysis of each human protein. Evidence scores use the ACMG/AMP Bayesian points scale with computable criteria only (position among known disease variants, rarity in gnomAD, calibrated predictors, deep mutational scanning); there is no family or patient data, so they prioritise variants for expert review and never classify them.

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