2q13 copy number variation syndrome (WP5222)

Homo sapiens

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The 2q13 copy number variation syndrome can result in the loss of up to 25 protein-coding genes. Patients with 2q13 deletions and duplications had abnormal head size and dysmorphic features (DOI: 10.1002/ajmg.a.37269). 2q13 duplications also caused developmental delay. The abnormal head size in 2q13 could be explained by the changes in FBLN7 gene (DOI: 10.1002/ajmg.a.37269). At the same time, neuropsychiatric impairment in 2q13 may be associated with BCL2L11, ANAPC1, SLC1A1 and MERTK alterations (DOI: 10.1002/ajmg.b.32236).

Authors

Daria Shumkova , Friederike Ehrhart , Eric Weitz , and Egon Willighagen

Activity

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Cited In

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Organisms

Homo sapiens

Communities

Rare Diseases

Annotations

Pathway Ontology

disease pathway

Disease Ontology

chromosomal deletion syndrome chromosomal duplication syndrome

Participants
Query Drugst.One

Label Type Compact URI Comment
Pi Metabolite chebi:43474
GDP Metabolite chebi:17552
FAD Metabolite chebi:57692
Na+ Metabolite chebi:29101
proteins Metabolite chebi:36080
GTP Metabolite chebi:37565
RPL5P9 GeneProduct ensembl:ENSG00000236330
MIR4435-1HG GeneProduct ensembl:ENSG00000172965
RPS14P4 GeneProduct ensembl:ENSG00000226928
MIR4435-2 GeneProduct ensembl:ENSG00000266139
MIR4435-1 GeneProduct ensembl:ENSG00000266139
MIR4771-1 GeneProduct ensembl:ENSG00000266063
MIR4771-2 GeneProduct ensembl:ENSG00000266063
HMGN2P23 GeneProduct ensembl:ENSG00000236124
RNU6-1180P GeneProduct ensembl:ENSG00000201805
POLR2L GeneProduct ensembl:ENSG00000177700
IL36RN GeneProduct ensembl:ENSG00000136695
POLR2K GeneProduct ensembl:ENSG00000147669
NT5DC4 GeneProduct ensembl:ENSG00000144130
BCL2L11 GeneProduct ensembl:ENSG00000153094
IL1B GeneProduct ensembl:ENSG00000125538
MERTK GeneProduct ensembl:ENSG00000153208
CKAP2L GeneProduct ensembl:ENSG00000169607
TTL GeneProduct ensembl:ENSG00000114999
POLR1D GeneProduct ensembl:ENSG00000186184
IL1RN GeneProduct ensembl:ENSG00000136689
IL36G GeneProduct ensembl:ENSG00000136688
IL1F10 GeneProduct ensembl:ENSG00000136697
POLR1A GeneProduct ensembl:ENSG00000068654
POLR1B GeneProduct ensembl:ENSG00000125630
IL1A GeneProduct ensembl:ENSG00000115008
ANAPC1 GeneProduct ensembl:ENSG00000153107
ACOXL GeneProduct ensembl:ENSG00000153093
PSD4 GeneProduct ensembl:ENSG00000125637
POLR2H GeneProduct ensembl:ENSG00000163882
FBLN7 GeneProduct ensembl:ENSG00000144152
RN7SL297P GeneProduct ensembl:ENSG00000240183
POLR2F GeneProduct ensembl:ENSG00000100142
RGPD8 GeneProduct ensembl:ENSG00000169629
TMEM87B GeneProduct ensembl:ENSG00000153214
POLR1E GeneProduct ensembl:ENSG00000137054
CHCHD5 GeneProduct ensembl:ENSG00000125611
POLR1G GeneProduct ensembl:ENSG00000117877
IL36A GeneProduct ensembl:ENSG00000136694
POLR1C GeneProduct ensembl:ENSG00000171453
IL37 GeneProduct ensembl:ENSG00000125571
PLCG2 GeneProduct ensembl:ENSG00000197943
POLR2E GeneProduct ensembl:ENSG00000099817
POLR1H GeneProduct ensembl:ENSG00000066379
ZC3H6 GeneProduct ensembl:ENSG00000188177
ZC3H8 GeneProduct ensembl:ENSG00000144161
SLC20A1 GeneProduct ensembl:ENSG00000144136
IL36B GeneProduct ensembl:ENSG00000136696
STAT1 GeneProduct ensembl:ENSG00000115415
POLR1F GeneProduct ensembl:ENSG00000105849
IL36RN Protein ensembl:ENSG00000136695
SOCS3 Protein ensembl:ENSG00000184557
TULP1 Protein ensembl:ENSG00000112041
IL2 Protein ensembl:ENSG00000109471
CSF1 Protein ensembl:ENSG00000184371
IL23A Protein ensembl:ENSG00000110944
GATA3 Protein ensembl:ENSG00000107485
GRB2 Protein ensembl:ENSG00000177885
CXCL13 Protein ensembl:ENSG00000156234
PTK2 Protein ensembl:ENSG00000169398
GAS6 Protein ensembl:ENSG00000183087
IL1R1 Protein ensembl:ENSG00000115594
SOCS1 Protein ensembl:ENSG00000185338
LGALS3 Protein ensembl:ENSG00000131981
CSF2 Protein ensembl:ENSG00000164400
IL1RL2 Protein ensembl:ENSG00000115598
IL1RAP Protein ensembl:ENSG00000196083
SLC20A1 Protein ensembl:ENSG00000144136
MAPK1 Protein ensembl:ENSG00000100030
ARF6 Protein ensembl:ENSG00000165527
ACOXL Protein ensembl:ENSG00000153093
IL6 Protein ensembl:ENSG00000136244
ARL14 Protein ensembl:ENSG00000179674
RAC1 Protein ensembl:ENSG00000136238

References

  1. The CoA esters of 2-methyl-branched chain fatty acids and of the bile acid intermediates di- and trihydroxycoprostanic acids are oxidized by one single peroxisomal branched chain acyl-CoA oxidase in human liver and kidney. Vanhove GF, Van Veldhoven PP, Fransen M, Denis S, Eyssen HJ, Wanders RJ, et al. J Biol Chem. 1993 May 15;268(14):10335–44. PubMed Europe PMC Scholia
  2. Molecular cloning of RPA2, the gene encoding the second largest subunit of mouse RNA polymerase I. Seither P, Grummt I. Genomics. 1996 Oct 1;37(1):135–9. PubMed Europe PMC Scholia
  3. Molecular characterization of the human peroxisomal branched-chain acyl-CoA oxidase: cDNA cloning, chromosomal assignment, tissue distribution, and evidence for the absence of the protein in Zellweger syndrome. Baumgart E, Vanhooren JC, Fransen M, Marynen P, Puype M, Vandekerckhove J, et al. Proc Natl Acad Sci U S A. 1996 Nov 26;93(24):13748–53. PubMed Europe PMC Scholia
  4. Identification of Gas6 as a ligand for Mer, a neural cell adhesion molecule related receptor tyrosine kinase implicated in cellular transformation. Chen J, Carey K, Godowski PJ. Oncogene. 1997 May 1;14(17):2033–9. PubMed Europe PMC Scholia
  5. Affinity purification of mammalian RNA polymerase I. Identification of an associated kinase. Hannan RD, Hempel WM, Cavanaugh A, Arino T, Dimitrov SI, Moss T, et al. J Biol Chem. 1998 Jan 9;273(2):1257–67. PubMed Europe PMC Scholia
  6. Bim: a novel member of the Bcl-2 family that promotes apoptosis. O’Connor L, Strasser A, O’Reilly LA, Hausmann G, Adams JM, Cory S, et al. EMBO J. 1998 Jan 15;17(2):384–95. PubMed Europe PMC Scholia
  7. FCP1, the RAP74-interacting subunit of a human protein phosphatase that dephosphorylates the carboxyl-terminal domain of RNA polymerase IIO. Archambault J, Pan G, Dahmus GK, Cartier M, Marshall N, Zhang S, et al. J Biol Chem. 1998 Oct 16;273(42):27593–601. PubMed Europe PMC Scholia
  8. Identification of a mammalian RNA polymerase I holoenzyme containing components of the DNA repair/replication system. Hannan RD, Cavanaugh A, Hempel WM, Moss T, Rothblum L. Nucleic Acids Res. 1999 Sep 15;27(18):3720–7. PubMed Europe PMC Scholia
  9. NaPO(4) cotransport type III (PiT1) expression in human embryonic kidney cells and regulation by PTH. Fernandes I, Béliveau R, Friedlander G, Silve C. Am J Physiol. 1999 Oct;277(4):F543-51. PubMed Europe PMC Scholia
  10. IL-12 synergizes with IL-18 or IL-1beta for IFN-gamma production from human T cells. Tominaga K, Yoshimoto T, Torigoe K, Kurimoto M, Matsui K, Hada T, et al. Int Immunol. 2000 Feb;12(2):151–60. PubMed Europe PMC Scholia
  11. Cytohesins and centaurins: mediators of PI 3-kinase-regulated Arf signaling. Jackson TR, Kearns BG, Theibert AB. Trends Biochem Sci. 2000 Oct;25(10):489–95. PubMed Europe PMC Scholia
  12. Anaphase-promoting complex/cyclosome-dependent proteolysis of human cyclin A starts at the beginning of mitosis and is not subject to the spindle assembly checkpoint. Geley S, Kramer E, Gieffers C, Gannon J, Peters JM, Hunt T. J Cell Biol. 2001 Apr 2;153(1):137–48. PubMed Europe PMC Scholia
  13. Molecular cloning and characterization of six novel isoforms of human Bim, a member of the proapoptotic Bcl-2 family. U M, Miyashita T, Shikama Y, Tadokoro K, Yamada M. FEBS Lett. 2001 Nov 30;509(1):135–41. PubMed Europe PMC Scholia
  14. Identification of novel isoforms of the BH3 domain protein Bim which directly activate Bax to trigger apoptosis. Marani M, Tenev T, Hancock D, Downward J, Lemoine NR. Mol Cell Biol. 2002 Jun;22(11):3577–89. PubMed Europe PMC Scholia
  15. Human securin proteolysis is controlled by the spindle checkpoint and reveals when the APC/C switches from activation by Cdc20 to Cdh1. Hagting A, Den Elzen N, Vodermaier HC, Waizenegger IC, Peters JM, Pines J. J Cell Biol. 2002 Jun 24;157(7):1125–37. PubMed Europe PMC Scholia
  16. Transcriptional regulation of GATA-3 by an intronic regulatory region and fetal liver zinc finger protein 1. Hwang ES, Choi A, Ho IC. J Immunol. 2002 Jul 1;169(1):248–53. PubMed Europe PMC Scholia
  17. A conserved C-terminal domain of EFA6-family ARF6-guanine nucleotide exchange factors induces lengthening of microvilli-like membrane protrusions. Derrien V, Couillault C, Franco M, Martineau S, Montcourrier P, Houlgatte R, et al. J Cell Sci. 2002 Jul 15;115(Pt 14):2867–79. PubMed Europe PMC Scholia
  18. B cell receptor-mediated apoptosis of human lymphocytes is associated with a new regulatory pathway of Bim isoform expression. Mouhamad S, Besnault L, Auffredou MT, Leprince C, Bourgeade MF, Leca G, et al. J Immunol. 2004 Feb 15;172(4):2084–91. PubMed Europe PMC Scholia
  19. Mechanism of RNA polymerase I transcription. Comai L. Adv Protein Chem. 2004;67:123–55. PubMed Europe PMC Scholia
  20. Over-expression of Bim alpha3, a novel isoform of human Bim, result in cell apoptosis. Chen JZ, Ji CN, Gu SH, Li JX, Zhao EP, Huang Y, et al. Int J Biochem Cell Biol. 2004 Aug;36(8):1554–61. PubMed Europe PMC Scholia
  21. Role of interleukin-8 in PiT-1 expression and CXCR1-mediated inorganic phosphate uptake in chondrocytes. Cecil DL, Rose DM, Terkeltaub R, Liu-Bryan R. Arthritis Rheum. 2005 Jan;52(1):144–54. PubMed Europe PMC Scholia
  22. Functional and mutational characterization of human MIA40 acting during import into the mitochondrial intermembrane space. Hofmann S, Rothbauer U, Mühlenbein N, Baiker K, Hell K, Bauer MF. J Mol Biol. 2005 Oct 28;353(3):517–28. PubMed Europe PMC Scholia
  23. Integrator, a multiprotein mediator of small nuclear RNA processing, associates with the C-terminal repeat of RNA polymerase II. Baillat D, Hakimi MA, Näär AM, Shilatifard A, Cooch N, Shiekhattar R. Cell. 2005 Oct 21;123(2):265–76. PubMed Europe PMC Scholia
  24. Signalling and functional diversity within the Axl subfamily of receptor tyrosine kinases. Hafizi S, Dahlbäck B. Cytokine Growth Factor Rev. 2006 Aug;17(4):295–304. PubMed Europe PMC Scholia
  25. Characterization of transport mechanisms and determinants critical for Na+-dependent Pi symport of the PiT family paralogs human PiT1 and PiT2. Bøttger P, Hede SE, Grunnet M, Høyer B, Klaerke DA, Pedersen L. Am J Physiol Cell Physiol. 2006 Dec;291(6):C1377-87. PubMed Europe PMC Scholia
  26. RNA polymerase I-specific subunit CAST/hPAF49 has a role in the activation of transcription by upstream binding factor. Panov KI, Panova TB, Gadal O, Nishiyama K, Saito T, Russell J, et al. Mol Cell Biol. 2006 Jul;26(14):5436–48. PubMed Europe PMC Scholia
  27. Efficient protein expression from the endogenous RNA polymerase I promoter using a human ribosomal DNA targeting vector. Wen L, Liang DS, Wu LQ, Cai F, Pan Q, Long ZG, et al. Biochem Biophys Res Commun. 2008 Mar 21;367(4):846–51. PubMed Europe PMC Scholia
  28. Immunobiology of the TAM receptors. Lemke G, Rothlin CV. Nat Rev Immunol. 2008 May;8(5):327–36. PubMed Europe PMC Scholia
  29. Mechanism of ubiquitin-chain formation by the human anaphase-promoting complex. Jin L, Williamson A, Banerjee S, Philipp I, Rape M. Cell. 2008 May 16;133(4):653–65. PubMed Europe PMC Scholia
  30. Identification of a novel function of PiT1 critical for cell proliferation and independent of its phosphate transport activity. Beck L, Leroy C, Salaün C, Margall-Ducos G, Desdouets C, Friedlander G. J Biol Chem. 2009 Nov 6;284(45):31363–74. PubMed Europe PMC Scholia
  31. The IL-1 family: regulators of immunity. Sims JE, Smith DE. Nat Rev Immunol. 2010 Feb;10(2):89–102. PubMed Europe PMC Scholia
  32. Tubby and tubby-like protein 1 are new MerTK ligands for phagocytosis. Caberoy NB, Zhou Y, Li W. EMBO J. 2010 Dec 1;29(23):3898–910. PubMed Europe PMC Scholia
  33. Mapping of the minimal inorganic phosphate transporting unit of human PiT2 suggests a structure universal to PiT-related proteins from all kingdoms of life. Bøttger P, Pedersen L. BMC Biochem. 2011 May 17;12:21. PubMed Europe PMC Scholia
  34. Galectin-3 is a new MerTK-specific eat-me signal. Caberoy NB, Alvarado G, Bigcas JL, Li W. J Cell Physiol. 2012 Feb;227(2):401–7. PubMed Europe PMC Scholia
  35. Structural basis of tubulin tyrosination by tubulin tyrosine ligase. Prota AE, Magiera MM, Kuijpers M, Bargsten K, Frey D, Wieser M, et al. J Cell Biol. 2013 Feb 4;200(3):259–70. PubMed Europe PMC Scholia
  36. The little elongation complex functions at initiation and elongation phases of snRNA gene transcription. Hu D, Smith ER, Garruss AS, Mohaghegh N, Varberg JM, Lin C, et al. Mol Cell. 2013 Aug 22;51(4):493–505. PubMed Europe PMC Scholia
  37. Human snRNA genes use polyadenylation factors to promote efficient transcription termination. O’Reilly D, Kuznetsova OV, Laitem C, Zaborowska J, Dienstbier M, Murphy S. Nucleic Acids Res. 2014 Jan;42(1):264–75. PubMed Europe PMC Scholia
  38. Radmis, a novel mitotic spindle protein that functions in cell division of neural progenitors. Yumoto T, Nakadate K, Nakamura Y, Sugitani Y, Sugitani-Yoshida R, Ueda S, et al. PLoS One. 2013 Nov 8;8(11):e79895. PubMed Europe PMC Scholia
  39. An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome. Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, et al. J Proteomics. 2014 Jan 16;96:253–62. PubMed Europe PMC Scholia
  40. Adult neuropsychiatric expression and familial segregation of 2q13 duplications. Costain G, Lionel AC, Fu F, Stavropoulos DJ, Gazzellone MJ, Marshall CR, et al. Am J Med Genet B Neuropsychiatr Genet. 2014 Jun;165B(4):337–44. PubMed Europe PMC Scholia
  41. Tumor-derived interleukin-1 promotes lymphangiogenesis and lymph node metastasis through M2-type macrophages. Watari K, Shibata T, Kawahara A, Sata K ichi, Nabeshima H, Shinoda A, et al. PLoS One. 2014 Jun 12;9(6):e99568. PubMed Europe PMC Scholia
  42. RPRD1A and RPRD1B are human RNA polymerase II C-terminal domain scaffolds for Ser5 dephosphorylation. Ni Z, Xu C, Guo X, Hunter GO, Kuznetsova OV, Tempel W, et al. Nat Struct Mol Biol. 2014 Aug;21(8):686–95. PubMed Europe PMC Scholia
  43. Molecular architecture and mechanism of the anaphase-promoting complex. Chang LF, Zhang Z, Yang J, McLaughlin SH, Barford D. Nature. 2014 Sep 18;513(7518):388–93. PubMed Europe PMC Scholia
  44. Mutations in CKAP2L, the human homolog of the mouse Radmis gene, cause Filippi syndrome. Hussain MS, Battaglia A, Szczepanski S, Kaygusuz E, Toliat MR, Sakakibara S ichi, et al. Am J Hum Genet. 2014 Nov 6;95(5):622–32. PubMed Europe PMC Scholia
  45. Mitosis. Microtubule detyrosination guides chromosomes during mitosis. Barisic M, Silva e Sousa R, Tripathy SK, Magiera MM, Zaytsev AV, Pereira AL, et al. Science. 2015 May 15;348(6236):799–803. PubMed Europe PMC Scholia
  46. Post-Golgi anterograde transport requires GARP-dependent endosome-to-TGN retrograde transport. Hirata T, Fujita M, Nakamura S, Gotoh K, Motooka D, Murakami Y, et al. Mol Biol Cell. 2015 Sep 1;26(17):3071–84. PubMed Europe PMC Scholia
  47. Recurrent deletions and duplications of chromosome 2q11.2 and 2q13 are associated with variable outcomes. Riley KN, Catalano LM, Bernat JA, Adams SD, Martin DM, Lalani SR, et al. Am J Med Genet A. 2015 Nov;167A(11):2664–73. PubMed Europe PMC Scholia
  48. Structure of the initiation-competent RNA polymerase I and its implication for transcription. Pilsl M, Crucifix C, Papai G, Krupp F, Steinbauer R, Griesenbeck J, et al. Nat Commun. 2016 Jul 15;7:12126. PubMed Europe PMC Scholia
  49. lnterleukin-1 Receptor Antagonist. Lennard AC. Crit Rev Immunol. 2017;37(2–6):531–59. PubMed Europe PMC Scholia
  50. Reviews of Interleukin-37: Functions, Receptors, and Roles in Diseases. Jia H, Liu J, Han B. Biomed Res Int. 2018 Apr 1;2018:3058640. PubMed Europe PMC Scholia
  51. Biology and regulation of IL-2: from molecular mechanisms to human therapy. Spolski R, Li P, Leonard WJ. Nat Rev Immunol. 2018 Oct;18(10):648–59. PubMed Europe PMC Scholia
  52. Biology and regulation of IL-2: from molecular mechanisms to human therapy. Spolski R, Li P, Leonard WJ. Nat Rev Immunol. 2018 Oct;18(10):648–59. PubMed Europe PMC Scholia
  53. Interleukin-36: Structure, Signaling and Function. Zhou L, Todorovic V. Adv Exp Med Biol. 2021;21:191–210. PubMed Europe PMC Scholia
  54. The role of adhesion protein Fibulin7 in development and diseases. Chakraborty P, Dash SP, Sarangi PP. Mol Med. 2020 May 19;26(1):47. PubMed Europe PMC Scholia
  55. Immunobiological Properties and Clinical Applications of Interleukin-38 for Immune-Mediated Disorders: A Systematic Review Study. Esmaeilzadeh A, Bahmaie N, Nouri E, Hajkazemi MJ, Zareh Rafie M. Int J Mol Sci. 2021 Nov 21;22(22):12552. PubMed Europe PMC Scholia