15q13.3 copy number variation syndrome (WP4942)

Homo sapiens

This pathway shows the genes deleted or duplicated in 15q13.3 copy number variation syndrome. The affected region is between 30,500,000-32,500,000 bp on Chromosome 15. The major genes in this region are OTUD7A and CHRNA7 which are known influencers of neuronal development and function. For several genes in this regio there are no exact functions known yet - e.g. the GOLGA gene group or the MTMR10 which is similar to phosphatidyl-inositol 3 phosphatases but without an active catalytic centre. The breakpoints 30,500,000-32,500,000 are from "15q13.3 Microdeletion", Bregje WM van Bon et al. in Gene reviews PMID: 20301295.

Authors

Friederike Ehrhart and Egon Willighagen

Activity

last edited

Discuss this pathway

Check for ongoing discussions or start your own.

Cited In

Are you planning to include this pathway in your next publication? See How to Cite and add a link here to your paper once it's online.

Organisms

Homo sapiens

Communities

Rare Diseases

Annotations

Disease Ontology

chromosome 15q13.3 microdeletion syndrome genetic disease

Pathway Ontology

disease pathway

Participants

Label Type Compact URI Comment
DNA Metabolite chebi:16991
Acetylcholine Metabolite chebi:15355
glutamate Metabolite chebi:14321
Alpha-Bungarotoxin Metabolite wikidata:Q1159221
RN7SL796P GeneProduct ensembl:ENSG00000277031
DNM1P50 GeneProduct ensembl:ENSG00000259890
ULK4P2 GeneProduct ensembl:ENSG00000260128
RN7SL628P GeneProduct ensembl:ENSG00000277467
GOLGA8UP GeneProduct ensembl:ENSG00000103832
RN7SL82P GeneProduct ensembl:ENSG00000278696
HERC2P10 GeneProduct ensembl:ENSG00000259845
RNU6-466P GeneProduct ensembl:ENSG00000212526
LINC02352 GeneProduct ensembl:ENSG00000259448
UBE2CP4 GeneProduct ensembl:ENSG00000259179
RNU6-18P GeneProduct ensembl:ENSG00000207257
RNU6-17P GeneProduct ensembl:ENSG00000206972
RN7SL196P GeneProduct ensembl:ENSG00000274424
KLF13 GeneProduct ensembl:ENSG00000169926
CHRNA7 GeneProduct ensembl:ENSG00000175344
MTMR10 GeneProduct ensembl:ENSG00000166912
GPR75 GeneProduct ensembl:ENSG00000119737
GOLGA8R GeneProduct ensembl:ENSG00000186399
CREBBP GeneProduct ensembl:ENSG00000005339
TRPM1 GeneProduct ensembl:ENSG00000134160
FANCD2 GeneProduct ensembl:ENSG00000144554
OTUD7A GeneProduct ensembl:ENSG00000169918
GOLGA8Q GeneProduct ensembl:ENSG00000178115
CHRFAM7A GeneProduct ensembl:ENSG00000166664
ARHGAP11B GeneProduct ensembl:ENSG00000285077
CCL5 GeneProduct ensembl:ENSG00000271503
FAN1 GeneProduct ensembl:ENSG00000198690
ADP/ATP translocases GeneProduct pfam:PF00153
GOLGA8H GeneProduct ensembl:ENSG00000261794
FYN GeneProduct ensembl:ENSG00000010810
GRM6 GeneProduct ensembl:ENSG00000113262
FANCD2 GeneProduct ensembl:ENSG00000144554
CCL5 GeneProduct ensembl:ENSG00000271503
SERPINH1 GeneProduct ensembl:ENSG00000149257
KAT2B GeneProduct ensembl:ENSG00000114166

References

  1. Normalization of auditory physiology by cigarette smoking in schizophrenic patients. Adler LE, Hoffer LD, Wiser A, Freedman R. Am J Psychiatry. 1993 Dec;150(12):1856–61. PubMed Europe PMC Scholia
  2. RFLAT-1: a new zinc finger transcription factor that activates RANTES gene expression in T lymphocytes. Song A, Chen YF, Thamatrakoln K, Storm TA, Krensky AM. Immunity. 1999 Jan;10(1):93–103. PubMed Europe PMC Scholia
  3. alpha 7 nicotinic receptor transduces signals to phosphatidylinositol 3-kinase to block A beta-amyloid-induced neurotoxicity. Kihara T, Shimohama S, Sawada H, Honda K, Nakamizo T, Shibasaki H, et al. J Biol Chem. 2001 Apr 27;276(17):13541–6. PubMed Europe PMC Scholia
  4. Functional interaction between coactivators CBP/p300, PCAF, and transcription factor FKLF2. Song CZ, Keller K, Murata K, Asano H, Stamatoyannopoulos G. J Biol Chem. 2002 Mar 1;277(9):7029–36. PubMed Europe PMC Scholia
  5. Alpha-bungarotoxin binding to acetylcholine receptor membranes studied by low angle X-ray diffraction. Young HS, Herbette LG, Skita V. Biophys J. 2003 Aug;85(2):943–53. PubMed Europe PMC Scholia
  6. RANTES stimulates Ca2+ mobilization and inositol trisphosphate (IP3) formation in cells transfected with G protein-coupled receptor 75. Ignatov A, Robert J, Gregory-Evans C, Schaller HC. Br J Pharmacol. 2006 Nov;149(5):490–7. PubMed Europe PMC Scholia
  7. Intronic miR-211 assumes the tumor suppressive function of its host gene in melanoma. Levy C, Khaled M, Iliopoulos D, Janas MM, Schubert S, Pinner S, et al. Mol Cell. 2010 Dec 10;40(5):841–9. PubMed Europe PMC Scholia
  8. Scan statistic-based analysis of exome sequencing data identifies FAN1 at 15q13.3 as a susceptibility gene for schizophrenia and autism. Ionita-Laza I, Xu B, Makarov V, Buxbaum JD, Roos JL, Gogos JA, et al. Proc Natl Acad Sci U S A. 2014 Jan 7;111(1):343–8. PubMed Europe PMC Scholia
  9. Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion. Florio M, Albert M, Taverna E, Namba T, Brandl H, Lewitus E, et al. Science. 2015 Mar 27;347(6229):1465–70. PubMed Europe PMC Scholia
  10. Properties and functions of TRPM1 channels in the dendritic tips of retinal ON-bipolar cells. Schneider FM, Mohr F, Behrendt M, Oberwinkler J. Eur J Cell Biol. 2015;94(7–9):420–7. PubMed Europe PMC Scholia
  11. Ubiquitinated Fancd2 recruits Fan1 to stalled replication forks to prevent genome instability. Lachaud C, Moreno A, Marchesi F, Toth R, Blow JJ, Rouse J. Science. 2016 Feb 19;351(6275):846–9. PubMed Europe PMC Scholia
  12. The Transduction Cascade in Retinal ON-Bipolar Cells: Signal Processing and Disease. Martemyanov KA, Sampath AP. Annu Rev Vis Sci. 2017 Sep 15;3:25–51. PubMed Europe PMC Scholia
  13. OTUD7A Regulates Neurodevelopmental Phenotypes in the 15q13.3 Microdeletion Syndrome. Uddin M, Unda BK, Kwan V, Holzapfel NT, White SH, Chalil L, et al. Am J Hum Genet. 2018 Feb 1;102(2):278–95. PubMed Europe PMC Scholia
  14. Human-Specific ARHGAP11B Acts in Mitochondria to Expand Neocortical Progenitors by Glutaminolysis. Namba T, Dóczi J, Pinson A, Xing L, Kalebic N, Wilsch-Bräuninger M, et al. Neuron. 2020 Mar 4;105(5):867-881.e9. PubMed Europe PMC Scholia