15q11.2 copy number variation syndrome (WP4940)

Homo sapiens

This pathway shows the genes known in the 15q11.2 region which can cause a copy number variation syndrome (CNV) if deleted or duplicated (or triplicated). These rare genetic syndromes are called 15q11.2 deletion or duplication syndrome, also known as Burnside Butler syndrome. This region is relatively small compared to other CNVs but it contains with NIPA1 and NIPA2 two important Magnesium transporters which are active in the central nervous system. CYFIP1 is an important interactor with FMR1, which is the causative gene for fragile X syndrome. The breakpoints (chr15:22,805,313-23,094,530 GRCh37/hg19) are defined as given in Kendall et al. 2017: https://doi.org/10.1016/j.biopsych.2016.08.014.


Friederike Ehrhart and Egon Willighagen


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Homo sapiens


Rare Diseases


Pathway Ontology

disease pathway

Disease Ontology

genetic disease chromosome 15q11.2 deletion syndrome


Label Type Compact URI Comment
Mg2+ Metabolite chebi:18420
ELMO2P1 GeneProduct ensembl:ENSG00000276172
TUBGCP5 GeneProduct ensembl:ENSG00000275835
NIPA2 GeneProduct ensembl:ENSG00000140157
TUBGCP6 GeneProduct ensembl:ENSG00000128159
TUBGCP4 GeneProduct ensembl:ENSG00000137822
TUBGCP2 GeneProduct ensembl:ENSG00000130640
NIPA1 GeneProduct ensembl:ENSG00000170113
CYFIP1 GeneProduct ensembl:ENSG00000273749
TUBGCP3 GeneProduct ensembl:ENSG00000126216
FMR1 GeneProduct ensembl:ENSG00000102081
TUBGCP5 GeneProduct ensembl:ENSG00000275835


  1. A highly conserved protein family interacting with the fragile X mental retardation protein (FMRP) and displaying selective interactions with FMRP-related proteins FXR1P and FXR2P. Schenck A, Bardoni B, Moro A, Bagni C, Mandel JL. Proc Natl Acad Sci U S A. 2001 Jul 17;98(15):8844–9. PubMed Europe PMC Scholia
  2. NIPA1(SPG6), the basis for autosomal dominant form of hereditary spastic paraplegia, encodes a functional Mg2+ transporter. Goytain A, Hines RM, El-Husseini A, Quamme GA. J Biol Chem. 2007 Mar 16;282(11):8060–8. PubMed Europe PMC Scholia
  3. Functional characterization of NIPA2, a selective Mg2+ transporter. Goytain A, Hines RM, Quamme GA. Am J Physiol Cell Physiol. 2008 Oct;295(4):C944-53. PubMed Europe PMC Scholia
  4. γ-Tubulin complexes in microtubule nucleation and beyond. Oakley BR, Paolillo V, Zheng Y. Mol Biol Cell. 2015 Sep 1;26(17):2957–62. PubMed Europe PMC Scholia