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Table 2 Biological processes significantly enriched among genes carrying a higher number of rare or low frequency variants in Dup7 carriers

From: Rare and low frequency genomic variants impacting neuronal functions modify the Dup7q11.23 phenotype

Outcome phenotype Variable Pathway category Pathway/function Number of genes in pathway Number of observed variants B (coefficient) P value FDR
BroadInd SS Likely damaging missense variants (5%) Neuroset Brain
Pre-natal (PC1 bottom 33%)
3038 451 − 2.75 3.10 × 10–3 0.078
CSS LoF variants (5%) Neuroset Brain low/absent expression 4601 145 0.574 3.19 × 10–3 0.078
LoF variants (5%) Neuroset Genic intolerance, very low (Q1) 4153 164 0.662 5.87 × 10–3 0.078
GCA LoF variants (1%) Neuroset Nervous System Development 1874 8 − 25.2 2.28 × 10–3 0.074
LoF variants (1%) GO Side of membrane [GO:0098552] 426 3 − 43.0 3.61 × 10–4 0.148
LoF variants (1%) GO External Side of Plasma Membrane [GO:0009897] 232 3 − 43.0 3.61 × 10–4 0.148
  1. CSS calibrated severity score (from ADOS-2), GCA General Conceptual Ability standard score (from DAS-II), GO gene ontology, LoF loss of function, PC1 principal component 1, BroadInd SS SIB-R Broad Independence standard score. Percentages in parentheses refer to variant frequency