3q29 copy number variation syndrome (WP4906)

Homo sapiens

3q29 copy number variation (duplication or deletion) is a rare genetic condition that results in a variety of psychiatric problems. The genes on the red DNA strand represents the deleted, or duplicated, region. The downstream effects and interaction partners of the different genes are shown according to available knowledge. The breakpoints (chr3:195,788,299 – 197,033,296, GRCh37/hg19) are defined as given in Cox and Butler PMID: 25714563.


Friederike Ehrhart , Egon Willighagen , Marvin Martens , and Pierre Klemmer


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.


Homo sapiens


Rare Diseases


Disease Ontology

disease of mental health chromosome 3q29 microduplication syndrome chromosomal disease chromosome 3q29 microdeletion syndrome

Pathway Ontology

disease pathway


Label Type Compact URI Comment
Choline phosphate(1−) Metabolite chebi:295975
Prostaglandin E2 Metabolite pubchem.compound:5280360
Digoxin Metabolite pubchem.compound:2724385
CTP4− Metabolite chebi:37563
O-phospho-L-serine(2−) residue Metabolite chebi:83421
Fe2+ Metabolite chebi:29033
Diphosphate(3−) Metabolite chebi:33019
Fe2+ Metabolite chebi:29033
L-serine residue Metabolite chebi:29999
S-palmitoyl-L-cysteine residueof a protein Metabolite chebi:74151
FRAX1036 Metabolite pubchem.compound:71557891
Taurocholic acid Metabolite pubchem.compound:6675
L-cysteine residueof a protein Metabolite chebi:29950
palmitoyl-CoA(4−) Metabolite chebi:57379
CoA Metabolite chebi:57287
Estrone sulfate Metabolite pubchem.compound:3001028
CDP-choline(1−) Metabolite chebi:58779
SDHAP1 GeneProduct ensembl:ENSG00000185485 pseudo gene
RNU6-910P GeneProduct ensembl:ENSG00000212146 pseudo gene
RNU6-1279P GeneProduct ensembl:ENSG00000206644 pseudo gene
RN7SL434P GeneProduct ensembl:ENSG00000241868 pseudo
RN7SL738P GeneProduct ensembl:ENSG00000243339 pseudo
RPS29P3 GeneProduct ensembl:ENSG00000225770 pseudo gene
RNU6-42P GeneProduct ensembl:ENSG00000206892 pseudo gene
RPSAP69 GeneProduct ensembl:ENSG00000233487 pseudo gene
DLG1 GeneProduct ensembl:ENSG00000075711
STAT5A GeneProduct ensembl:ENSG00000126561
ZNF76 GeneProduct ensembl:ENSG00000065029
RNF8 GeneProduct ensembl:ENSG00000112130
MYC GeneProduct ensembl:ENSG00000136997
CEP350 GeneProduct ensembl:ENSG00000135837
FGFR1OP GeneProduct ensembl:ENSG00000213066
BRINP1 GeneProduct ensembl:ENSG00000078725 DBC1
MYCBP2 GeneProduct ensembl:ENSG00000005810
PAK2 GeneProduct ensembl:ENSG00000180370
MELTF GeneProduct ensembl:ENSG00000163975
FBXO45 GeneProduct ensembl:ENSG00000174013
TM4SF19 GeneProduct ensembl:ENSG00000145107
TGFB1 GeneProduct ensembl:ENSG00000105329
WDR60 GeneProduct ensembl:ENSG00000126870
PIK3R3 GeneProduct ensembl:ENSG00000117461
UBE2N GeneProduct ensembl:ENSG00000177889
CEP19 GeneProduct ensembl:ENSG00000174007
RNU2-11P GeneProduct ensembl:ENSG00000239122 pseudo gene
SMCO1 GeneProduct ensembl:ENSG00000214097
HAMP GeneProduct ensembl:ENSG00000105697
SLC51A GeneProduct ensembl:ENSG00000163959 OSTA, OSTalpha
STAT5B GeneProduct ensembl:ENSG00000173757
PXN GeneProduct ensembl:ENSG00000089159
TFRC GeneProduct ensembl:ENSG00000072274
RNU7-18P GeneProduct ensembl:ENSG00000252174 pseudo gene
GRIA1 GeneProduct ensembl:ENSG00000155511 GluR1
SLC51B GeneProduct ensembl:ENSG00000186198 OSTB, OSTbeta
WDR53 GeneProduct ensembl:ENSG00000185798
NCBP2 GeneProduct ensembl:ENSG00000114503
PIGX GeneProduct ensembl:ENSG00000163964
NRROS GeneProduct ensembl:ENSG00000174004 LRRC33
TCTEX1D2 GeneProduct ensembl:ENSG00000213123
SIRT1 GeneProduct ensembl:ENSG00000096717
DYNC2LI1 GeneProduct ensembl:ENSG00000138036
SLC40A1 GeneProduct ensembl:ENSG00000138449 Ferroportin
FNDC8 GeneProduct ensembl:ENSG00000073598
MCRS1 GeneProduct ensembl:ENSG00000187778
ADAM10 GeneProduct ensembl:ENSG00000137845
JUN GeneProduct ensembl:ENSG00000177606
PIGZ GeneProduct ensembl:ENSG00000119227
RNF168 GeneProduct ensembl:ENSG00000163961
NF2 GeneProduct ensembl:ENSG00000186575 merlin
HFE GeneProduct ensembl:ENSG00000010704
TF GeneProduct ensembl:ENSG00000091513 Transferrin
FBXW7 GeneProduct ensembl:ENSG00000109670
RNU6-646P GeneProduct ensembl:ENSG00000201441 pseudo gene
SENP5 GeneProduct ensembl:ENSG00000119231
MAD2L1BP GeneProduct ensembl:ENSG00000124688
ZDHHC19 GeneProduct ensembl:ENSG00000163958 Palmitoyltransferase
RNU4-89P GeneProduct ensembl:ENSG00000272359 pseudo gene
CASP7 GeneProduct ensembl:ENSG00000165806
PIGM GeneProduct ensembl:ENSG00000143315
UBXN7 GeneProduct ensembl:ENSG00000163960
PCYT1A GeneProduct ensembl:ENSG00000161217
NCBP1 GeneProduct ensembl:ENSG00000136937
DYNC2H1 GeneProduct ensembl:ENSG00000187240
HIF1A GeneProduct ensembl:ENSG00000100644
RABL2B GeneProduct ensembl:ENSG00000079974
SLC51A GeneProduct ensembl:ENSG00000163959 OSTA, OSTalpha
WDR34 GeneProduct ensembl:ENSG00000119333
TCTEX1D2 GeneProduct ensembl:ENSG00000213123
DYNLT1 GeneProduct ensembl:ENSG00000146425
TCTEX1D2 GeneProduct ensembl:ENSG00000213123
DYNLT3 GeneProduct ensembl:ENSG00000165169
DYNLRB1 GeneProduct ensembl:ENSG00000125971
DYNLRB2 GeneProduct ensembl:ENSG00000168589
DYNLL1 GeneProduct ensembl:ENSG00000088986
DYNLL2 GeneProduct ensembl:ENSG00000264364
DYNC2LI1 GeneProduct ensembl:ENSG00000138036
DYNC2H1 GeneProduct ensembl:ENSG00000187240
AKT1 GeneProduct ensembl:ENSG00000142208
HIF1A GeneProduct ensembl:ENSG00000100644
RNF168 GeneProduct ensembl:ENSG00000163961
FBXO45 GeneProduct ensembl:ENSG00000174013
PIGX GeneProduct ensembl:ENSG00000163964
STAT5A GeneProduct ensembl:ENSG00000126561
MYC GeneProduct ensembl:ENSG00000136997
STAT5B GeneProduct ensembl:ENSG00000173757
PXN GeneProduct ensembl:ENSG00000089159
JUN GeneProduct ensembl:ENSG00000177606
NF2 GeneProduct ensembl:ENSG00000186575 merlin
CASP7 GeneProduct ensembl:ENSG00000165806
BRINP1 GeneProduct ensembl:ENSG00000078725 DBC1
BRINP1 GeneProduct ensembl:ENSG00000078725 DBC1
NCBP2 GeneProduct ensembl:ENSG00000114503


  1. Molecular cloning and characterisation of a novel putative protein-serine kinase related to the cAMP-dependent and protein kinase C families. Coffer PJ, Woodgett JR. Eur J Biochem. 1991 Oct 15;201(2):475–81. PubMed Europe PMC Scholia
  2. Molecular cloning and identification of a serine/threonine protein kinase of the second-messenger subfamily. Jones PF, Jakubowicz T, Pitossi FJ, Maurer F, Hemmings BA. Proc Natl Acad Sci U S A. 1991 May 15;88(10):4171–5. PubMed Europe PMC Scholia
  3. A novel iron uptake mechanism mediated by GPI-anchored human p97. Kennard ML, Richardson DR, Gabathuler R, Ponka P, Jefferies WA. EMBO J. 1995 Sep 1;14(17):4178–86. PubMed Europe PMC Scholia
  4. The hemochromatosis gene product complexes with the transferrin receptor and lowers its affinity for ligand binding. Feder JN, Penny DM, Irrinki A, Lee VK, Lebrón JA, Watson N, et al. Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1472–7. PubMed Europe PMC Scholia
  5. SAP97 is associated with the alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid receptor GluR1 subunit. Leonard AS, Davare MA, Horne MC, Garner CC, Hell JW. J Biol Chem. 1998 Jul 31;273(31):19518–24. PubMed Europe PMC Scholia
  6. The role of histidine residues in the HXGH site of CTP:phosphocholine cytidylyltransferase in CTP binding and catalysis. Veitch DP, Gilham D, Cornell RB. Eur J Biochem. 1998 Jul 1;255(1):227–34. PubMed Europe PMC Scholia
  7. Comparison of the interactions of transferrin receptor and transferrin receptor 2 with transferrin and the hereditary hemochromatosis protein HFE. West AP Jr, Bennett MJ, Sellers VM, Andrews NC, Enns CA, Bjorkman PJ. J Biol Chem. 2000 Dec 8;275(49):38135–8. PubMed Europe PMC Scholia
  8. Crystal structure of the human nuclear cap binding complex. Mazza C, Ohno M, Segref A, Mattaj IW, Cusack S. Mol Cell. 2001 Aug;8(2):383–96. PubMed Europe PMC Scholia
  9. Identification of lysine 122 and arginine 196 as important functional residues of rat CTP:phosphocholine cytidylyltransferase alpha. Helmink BA, Braker JD, Kent C, Friesen JA. Biochemistry. 2003 May 6;42(17):5043–51. PubMed Europe PMC Scholia
  10. Functional complementation between a novel mammalian polygenic transport complex and an evolutionarily ancient organic solute transporter, OSTalpha-OSTbeta. Seward DJ, Koh AS, Boyer JL, Ballatori N. J Biol Chem. 2003 Jul 25;278(30):27473–82. PubMed Europe PMC Scholia
  11. Negative control of the Myc protein by the stress-responsive kinase Pak2. Huang Z, Traugh JA, Bishop JM. Mol Cell Biol. 2004 Feb;24(4):1582–94. PubMed Europe PMC Scholia
  12. Human Smp3p adds a fourth mannose to yeast and human glycosylphosphatidylinositol precursors in vivo. Taron BW, Colussi PA, Wiedman JM, Orlean P, Taron CH. J Biol Chem. 2004 Aug 20;279(34):36083–92. PubMed Europe PMC Scholia
  13. Serine 518 phosphorylation modulates merlin intramolecular association and binding to critical effectors important for NF2 growth suppression. Rong R, Surace EI, Haipek CA, Gutmann DH, Ye K. Oncogene. 2004 Nov 4;23(52):8447–54. PubMed Europe PMC Scholia
  14. The heteromeric organic solute transporter alpha-beta, Ostalpha-Ostbeta, is an ileal basolateral bile acid transporter. Dawson PA, Hubbert M, Haywood J, Craddock AL, Zerangue N, Christian WV, et al. J Biol Chem. 2005 Feb 25;280(8):6960–8. PubMed Europe PMC Scholia
  15. Mammalian PIG-X and yeast Pbn1p are the essential components of glycosylphosphatidylinositol-mannosyltransferase I. Ashida H, Hong Y, Murakami Y, Shishioh N, Sugimoto N, Kim YU, et al. Mol Biol Cell. 2005 Mar;16(3):1439–48. PubMed Europe PMC Scholia
  16. Regulation of iron metabolism by hepcidin. Nemeth E, Ganz T. Annu Rev Nutr. 2006;26:323–42. PubMed Europe PMC Scholia
  17. DBC1 is a negative regulator of SIRT1. Kim JE, Chen J, Lou Z. Nature. 2008 Jan 31;451(7178):583–6. PubMed Europe PMC Scholia
  18. Negative regulation of the deacetylase SIRT1 by DBC1. Zhao W, Kruse JP, Tang Y, Jung SY, Qin J, Gu W. Nature. 2008 Jan 31;451(7178):587–90. PubMed Europe PMC Scholia
  19. UBXD7 binds multiple ubiquitin ligases and implicates p97 in HIF1alpha turnover. Alexandru G, Graumann J, Smith GT, Kolawa NJ, Fang R, Deshaies RJ. Cell. 2008 Sep 5;134(5):804–16. PubMed Europe PMC Scholia
  20. The RIDDLE syndrome protein mediates a ubiquitin-dependent signaling cascade at sites of DNA damage. Stewart GS, Panier S, Townsend K, Al-Hakim AK, Kolas NK, Miller ES, et al. Cell. 2009 Feb 6;136(3):420–34. PubMed Europe PMC Scholia
  21. Palmitoylation of R-Ras by human DHHC19, a palmitoyl transferase with a CaaX box. Baumgart F, Corral-Escariz M, Pérez-Gil J, Rodríguez-Crespo I. Biochim Biophys Acta. 2010 Mar;1798(3):592–604. PubMed Europe PMC Scholia
  22. Getting the mOST from OST: Role of organic solute transporter, OSTalpha-OSTbeta, in bile acid and steroid metabolism. Dawson PA, Hubbert ML, Rao A. Biochim Biophys Acta. 2010 Sep;1801(9):994–1004. PubMed Europe PMC Scholia
  23. P21-activated protein kinase (PAK2)-mediated c-Jun phosphorylation at 5 threonine sites promotes cell transformation. Li T, Zhang J, Zhu F, Wen W, Zykova T, Li X, et al. Carcinogenesis. 2011 May;32(5):659–66. PubMed Europe PMC Scholia
  24. Phosphorylation of caspase-7 by p21-activated protein kinase (PAK) 2 inhibits chemotherapeutic drug-induced apoptosis of breast cancer cell lines. Li X, Wen W, Liu K, Zhu F, Malakhova M, Peng C, et al. J Biol Chem. 2011 Jun 24;286(25):22291–9. PubMed Europe PMC Scholia
  25. UBXN7 docks on neddylated cullin complexes using its UIM motif and causes HIF1α accumulation. Bandau S, Knebel A, Gage ZO, Wood NT, Alexandru G. BMC Biol. 2012 Apr 26;10:36. PubMed Europe PMC Scholia
  26. HIV Nef, paxillin, and Pak1/2 regulate activation and secretion of TACE/ADAM10 proteases. Lee JH, Wittki S, Bräu T, Dreyer FS, Krätzel K, Dindorf J, et al. Mol Cell. 2013 Feb 21;49(4):668–79. PubMed Europe PMC Scholia
  27. The ATM signaling network in development and disease. Stracker TH, Roig I, Knobel PA, Marjanović M. Front Genet. 2013 Mar 25;4:37. PubMed Europe PMC Scholia
  28. FRAX597, a small molecule inhibitor of the p21-activated kinases, inhibits tumorigenesis of neurofibromatosis type 2 (NF2)-associated Schwannomas. Licciulli S, Maksimoska J, Zhou C, Troutman S, Kota S, Liu Q, et al. J Biol Chem. 2013 Oct 4;288(40):29105–14. PubMed Europe PMC Scholia
  29. PAK-dependent STAT5 serine phosphorylation is required for BCR-ABL-induced leukemogenesis. Berger A, Hoelbl-Kovacic A, Bourgeais J, Hoefling L, Warsch W, Grundschober E, et al. Leukemia. 2014 Mar;28(3):629–41. PubMed Europe PMC Scholia
  30. Modification of DBC1 by SUMO2/3 is crucial for p53-mediated apoptosis in response to DNA damage. Park JH, Lee SW, Yang SW, Yoo HM, Park JM, Seong MW, et al. Nat Commun. 2014 Nov 18;5:5483. PubMed Europe PMC Scholia
  31. Pak2 regulates hematopoietic progenitor cell proliferation, survival, and differentiation. Zeng Y, Broxmeyer HE, Staser K, Chitteti BR, Park SJ, Hahn S, et al. Stem Cells. 2015 May;33(5):1630–41. PubMed Europe PMC Scholia
  32. Small molecule inhibition of group I p21-activated kinases in breast cancer induces apoptosis and potentiates the activity of microtubule stabilizing agents. Ong CC, Gierke S, Pitt C, Sagolla M, Cheng CK, Zhou W, et al. Breast Cancer Res. 2015 Apr 23;17(1):59. PubMed Europe PMC Scholia
  33. TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport. Schmidts M, Hou Y, Cortés CR, Mans DA, Huber C, Boldt K, et al. Nat Commun. 2015 Jun 5;6:7074. PubMed Europe PMC Scholia
  34. RABL2 interacts with the intraflagellar transport-B complex and CEP19 and participates in ciliary assembly. Nishijima Y, Hagiya Y, Kubo T, Takei R, Katoh Y, Nakayama K. Mol Biol Cell. 2017 Jun 15;28(12):1652–66. PubMed Europe PMC Scholia
  35. The CEP19-RABL2 GTPase Complex Binds IFT-B to Initiate Intraflagellar Transport at the Ciliary Base. Kanie T, Abbott KL, Mooney NA, Plowey ED, Demeter J, Jackson PK. Dev Cell. 2017 Jul 10;42(1):22-36.e12. PubMed Europe PMC Scholia
  36. CEP19 cooperates with FOP and CEP350 to drive early steps in the ciliogenesis programme. Mojarad BA, Gupta GD, Hasegan M, Goudiam O, Basto R, Gingras AC, et al. Open Biol. 2017 Jun;7(6):170114. PubMed Europe PMC Scholia
  37. A Milieu Molecule for TGF-β Required for Microglia Function in the Nervous System. Qin Y, Garrison BS, Ma W, Wang R, Jiang A, Li J, et al. Cell. 2018 Jun 28;174(1):156-171.e16. PubMed Europe PMC Scholia
  38. Host and parasite responses in human diffuse cutaneous leishmaniasis caused by L. amazonensis. Christensen SM, Belew AT, El-Sayed NM, Tafuri WL, Silveira FT, Mosser DM. PLoS Negl Trop Dis. 2019 Mar 7;13(3):e0007152. PubMed Europe PMC Scholia
  39. FBXO45-MYCBP2 regulates mitotic cell fate by targeting FBXW7 for degradation. Richter KT, Kschonsak YT, Vodicska B, Hoffmann I. Cell Death Differ. 2020 Feb;27(2):758–72. PubMed Europe PMC Scholia
  40. A reference map of the human binary protein interactome. Luck K, Kim DK, Lambourne L, Spirohn K, Begg BE, Bian W, et al. Nature. 2020 Apr;580(7803):402–8. PubMed Europe PMC Scholia