3q29 copy number variation syndrome (Homo sapiens)

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141931215821124, 1621201, 211919139, 105, 1121186172Proposed model of IFT dynein compositionBile acid transportand uptakaChromosome 3:195,788,299phosphorylated statelittle information available:upregulated in regulatory macrophages during Leishmania infectionRegulation of Iron uptakePalmitoylationcatalysesphoshporylationon tyrosineControls phosphatidylcholine synthesisRNA gene7SLC40A1Estrone sulfateRPSAP69L-cysteine residueof a proteinRNU6-910PDLG1LINC01983NCBP2AS2RNU6-42PCholine phosphate(1−)WDR60Prostaglandin E2hsa-mir-4797Fe2+RNU7-18PCTP4−PAK2palmitoyl-CoA(4−)PIGZNCBP2ATMSLC51AMELTF-AS1SMCO1CDP-choline(1−)S-palmitoyl-L-cysteine residueof a proteinRN7SL738PWWOXTM4SF19-AS1AKT1WDR53FYNRNU2-11PMIR6829DNA Double Strand Break ResponseDiphosphate(3−)CoARNF168TM4SF19-TCTEX1D2UBXN7SDHAP1DigoxinMUC4TNK2TFRPS29P3LINC01063TFRCGRB2RN7SL434PTNK2-AS1RNU6-646PSLC51BApoptosis PIGXLINC00885CEP19DYNC2LI1TCTEX1D2HFEZDHHC19DLG1-AS1ERBB2HAMPNRROSTaurocholic acidARPCYT1AFBXO45RNU4-89PKIF3AP1NCBP2-AS1MELTFTM4SF19RNU6-1279PHIF1AUBXN7-AS1SENP5DYNC2H1Chromosome 3:197,033,296AKT1ARWWOXFYNGRB2pseudo gene2120SLC51A888151515WDR34TCTEX1D2DYNLT1TCTEX1D2DYNLT3DYNLRB1DYNLRB2DYNLL1DYNLL2DYNC2LI1DYNC2H1AKT1HIF1AUUubiquitinated state


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.

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  1. Feder JN, Penny DM, Irrinki A, Lee VK, Lebrón JA, Watson N, Tsuchihashi Z, Sigal E, Bjorkman PJ, Schatzman RC; ''The hemochromatosis gene product complexes with the transferrin receptor and lowers its affinity for ligand binding.''; Proc Natl Acad Sci U S A, 1998 PubMed Europe PMC Scholia
  2. Linseman DA, Heidenreich KA, Fisher SK; ''Stimulation of M3 muscarinic receptors induces phosphorylation of the Cdc42 effector activated Cdc42Hs-associated kinase-1 via a Fyn tyrosine kinase signaling pathway.''; J Biol Chem, 2001 PubMed Europe PMC Scholia
  3. Schmidts M, Hou Y, Cortés CR, Mans DA, Huber C, Boldt K, Patel M, van Reeuwijk J, Plaza JM, van Beersum SE, Yap ZM, Letteboer SJ, Taylor SP, Herridge W, Johnson CA, Scambler PJ, Ueffing M, Kayserili H, Krakow D, King SM, Beales PL, Al-Gazali L, Wicking C, Cormier-Daire V, Roepman R, Mitchison HM, Witman GB; ''TCTEX1D2 mutations underlie Jeune asphyxiating thoracic dystrophy with impaired retrograde intraflagellar transport.''; Nat Commun, 2015 PubMed Europe PMC Scholia
  4. Alexandru G, Graumann J, Smith GT, Kolawa NJ, Fang R, Deshaies RJ; ''UBXD7 binds multiple ubiquitin ligases and implicates p97 in HIF1alpha turnover.''; Cell, 2008 PubMed Europe PMC Scholia
  5. Dawson PA, Hubbert M, Haywood J, Craddock AL, Zerangue N, Christian WV, Ballatori N; ''The heteromeric organic solute transporter alpha-beta, Ostalpha-Ostbeta, is an ileal basolateral bile acid transporter.''; J Biol Chem, 2005 PubMed Europe PMC Scholia
  6. Mahajan NP, Liu Y, Majumder S, Warren MR, Parker CE, Mohler JL, Earp HS, Whang YE; ''Activated Cdc42-associated kinase Ack1 promotes prostate cancer progression via androgen receptor tyrosine phosphorylation.''; Proc Natl Acad Sci U S A, 2007 PubMed Europe PMC Scholia
  7. Christensen SM, Belew AT, El-Sayed NM, Tafuri WL, Silveira FT, Mosser DM; ''Host and parasite responses in human diffuse cutaneous leishmaniasis caused by L. amazonensis.''; PLoS Negl Trop Dis, 2019 PubMed Europe PMC Scholia
  8. Veitch DP, Gilham D, Cornell RB; ''The role of histidine residues in the HXGH site of CTP:phosphocholine cytidylyltransferase in CTP binding and catalysis.''; Eur J Biochem, 1998 PubMed Europe PMC Scholia
  9. Kato-Stankiewicz J, Ueda S, Kataoka T, Kaziro Y, Satoh T; ''Epidermal growth factor stimulation of the ACK1/Dbl pathway in a Cdc42 and Grb2-dependent manner.''; Biochem Biophys Res Commun, 2001 PubMed Europe PMC Scholia
  10. Satoh T, Kato J, Nishida K, Kaziro Y; ''Tyrosine phosphorylation of ACK in response to temperature shift-down, hyperosmotic shock, and epidermal growth factor stimulation.''; FEBS Lett, 1996 PubMed Europe PMC Scholia
  11. Seward DJ, Koh AS, Boyer JL, Ballatori N; ''Functional complementation between a novel mammalian polygenic transport complex and an evolutionarily ancient organic solute transporter, OSTalpha-OSTbeta.''; J Biol Chem, 2003 PubMed Europe PMC Scholia
  12. Carraway KL, Perez A, Idris N, Jepson S, Arango M, Komatsu M, Haq B, Price-Schiavi SA, Zhang J, Carraway CA; ''Muc4/sialomucin complex, the intramembrane ErbB2 ligand, in cancer and epithelia: to protect and to survive.''; Prog Nucleic Acid Res Mol Biol, 2002 PubMed Europe PMC Scholia
  13. Mahajan NP, Whang YE, Mohler JL, Earp HS; ''Activated tyrosine kinase Ack1 promotes prostate tumorigenesis: role of Ack1 in polyubiquitination of tumor suppressor Wwox.''; Cancer Res, 2005 PubMed Europe PMC Scholia
  14. Mahajan K, Coppola D, Rawal B, Chen YA, Lawrence HR, Engelman RW, Lawrence NJ, Mahajan NP; ''Ack1-mediated androgen receptor phosphorylation modulates radiation resistance in castration-resistant prostate cancer.''; J Biol Chem, 2012 PubMed Europe PMC Scholia
  15. Helmink BA, Braker JD, Kent C, Friesen JA; ''Identification of lysine 122 and arginine 196 as important functional residues of rat CTP:phosphocholine cytidylyltransferase alpha.''; Biochemistry, 2003 PubMed Europe PMC Scholia
  16. Bandau S, Knebel A, Gage ZO, Wood NT, Alexandru G; ''UBXN7 docks on neddylated cullin complexes using its UIM motif and causes HIF1α accumulation.''; BMC Biol, 2012 PubMed Europe PMC Scholia
  17. Mahajan K, Coppola D, Challa S, Fang B, Chen YA, Zhu W, Lopez AS, Koomen J, Engelman RW, Rivera C, Muraoka-Cook RS, Cheng JQ, Schönbrunn E, Sebti SM, Earp HS, Mahajan NP; ''Ack1 mediated AKT/PKB tyrosine 176 phosphorylation regulates its activation.''; PLoS One, 2010 PubMed Europe PMC Scholia
  18. Dawson PA, Hubbert ML, Rao A; ''Getting the mOST from OST: Role of organic solute transporter, OSTalpha-OSTbeta, in bile acid and steroid metabolism.''; Biochim Biophys Acta, 2010 PubMed Europe PMC Scholia
  19. Nemeth E, Ganz T; ''Regulation of iron metabolism by hepcidin.''; Annu Rev Nutr, 2006 PubMed Europe PMC Scholia
  20. Baumgart F, Corral-Escariz M, Pérez-Gil J, Rodríguez-Crespo I; ''Palmitoylation of R-Ras by human DHHC19, a palmitoyl transferase with a CaaX box.''; Biochim Biophys Acta, 2010 PubMed Europe PMC Scholia
  21. West AP Jr, Bennett MJ, Sellers VM, Andrews NC, Enns CA, Bjorkman PJ; ''Comparison of the interactions of transferrin receptor and transferrin receptor 2 with transferrin and the hereditary hemochromatosis protein HFE.''; J Biol Chem, 2000 PubMed Europe PMC Scholia


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110586view11:15, 19 May 2020Fehrhartwork in progress
110580view10:46, 19 May 2020Fehrhartwork in progress
110578view10:18, 19 May 2020Fehrhartwork in progress
110317view22:18, 3 May 2020Marvin M2Ontology Term : 'chromosomal disease' added !
110316view22:17, 3 May 2020Marvin M2Ontology Term : 'chromosome 3q29 microduplication syndrome' added !
110315view22:17, 3 May 2020Marvin M2Ontology Term : 'chromosome 3q29 microdeletion syndrome' added !
110304view06:42, 3 May 2020EgonwReplaced a secondary ChEBI identifiers with a primary identifier.
110269view12:44, 1 May 2020Fehrhartadded reference
110268view12:26, 1 May 2020Fehrhartwork in progress
110251view10:40, 30 April 2020Fehrhartwork in progress
110250view10:28, 30 April 2020Fehrhartwork in progress (TFRC)
110176view09:19, 23 April 2020Fehrhartwork in progress
110161view08:54, 22 April 2020FehrhartOntology Term : 'disease of mental health' added !
110160view08:54, 22 April 2020FehrhartOntology Term : 'disease pathway' added !
110159view08:53, 22 April 2020FehrhartModified description
110158view08:49, 22 April 2020FehrhartWork in progress
110147view06:47, 21 April 2020FehrhartNew pathway

External references


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NameTypeDatabase referenceComment
AKT1GeneProductENSG00000142208 (Ensembl)
ARGeneProductENSG00000169083 (Ensembl) NR3C4
ATMGeneProductENSG00000149311 (Ensembl)
Apoptosis PathwayWP254 (WikiPathways)
CDP-choline(1−)Metabolite58779 (ChEBI)
CEP19GeneProductENSG00000174007 (Ensembl)
CTP4−Metabolite37563 (ChEBI)
Choline phosphate(1−)Metabolite295975 (ChEBI)
CoAMetabolite57287 (ChEBI)
DLG1-AS1RnaENSG00000227375 (Ensembl) ncRNA
DLG1GeneProductENSG00000075711 (Ensembl)
DNA Double Strand Break ResponsePathwayWP3543 (WikiPathways)
DYNC2H1GeneProductENSG00000187240 (Ensembl)
DYNC2LI1GeneProductENSG00000138036 (Ensembl)
DYNLL1GeneProductENSG00000088986 (Ensembl)
DYNLL2GeneProductENSG00000264364 (Ensembl)
DYNLRB1GeneProductENSG00000125971 (Ensembl)
DYNLRB2GeneProductENSG00000168589 (Ensembl)
DYNLT1GeneProductENSG00000146425 (Ensembl)
DYNLT3GeneProductENSG00000165169 (Ensembl)
DigoxinMetabolite2724385 (PubChem-compound)
Diphosphate(3−)Metabolite33019 (ChEBI)
ERBB2GeneProductENSG00000141736 (Ensembl)
Estrone sulfateMetabolite3001028 (PubChem-compound)
FBXO45GeneProductENSG00000174013 (Ensembl)
FYNGeneProductENSG00000010810 (Ensembl)
Fe2+MetaboliteCHEBI:29033 (ChEBI)
GRB2GeneProductENSG00000177885 (Ensembl)
HAMPGeneProductENSG00000105697 (Ensembl)
HFEGeneProductENSG00000010704 (Ensembl)
HIF1AGeneProductENSG00000100644 (Ensembl)
KIF3AP1GeneProductENSG00000235836 (Ensembl) pseudo gene
L-cysteine residue of a proteinMetabolite29950 (ChEBI)
LINC00885RnaENSG00000224652 (Ensembl) ncRNA
LINC01063RnaENSG00000232065 (Ensembl) ncRNA
LINC01983RnaENSG00000223783 (Ensembl) ncRNA
MELTF-AS1RnaENSG00000228109 (Ensembl) ncRNA
MELTFGeneProductENSG00000163975 (Ensembl)
MIR6829RnaENSG00000276489 (Ensembl)
MUC4GeneProductENSG00000145113 (Ensembl)
NCBP2-AS1RnaENSG00000225578 (Ensembl) ncRNA
NCBP2AS2RnaENSG00000270170 (Ensembl) ncRNA
NCBP2GeneProductENSG00000114503 (Ensembl)
NRROSGeneProductENSG00000174004 (Ensembl)
PAK2GeneProductENSG00000180370 (Ensembl)
PCYT1AGeneProductENSG00000161217 (Ensembl)
PIGXGeneProductENSG00000163964 (Ensembl)
PIGZGeneProductENSG00000119227 (Ensembl)
Prostaglandin E2Metabolite5280360 (PubChem-compound)
RN7SL434PGeneProductENSG00000241868 (Ensembl) pseudo
RN7SL738PGeneProductENSG00000243339 (Ensembl) pseudo
RNF168GeneProductENSG00000163961 (Ensembl)
RNU2-11PGeneProductENSG00000239122 (Ensembl) pseudo gene
RNU4-89PGeneProductENSG00000272359 (Ensembl) pseudo gene
RNU6-1279PGeneProductENSG00000206644 (Ensembl) pseudo gene
RNU6-42PGeneProductENSG00000206892 (Ensembl) pseudo gene
RNU6-646PGeneProductENSG00000201441 (Ensembl) pseudo gene
RNU6-910PGeneProductENSG00000212146 (Ensembl) pseudo gene
RNU7-18PGeneProductENSG00000252174 (Ensembl) pseudo gene
RPS29P3GeneProductENSG00000225770 (Ensembl) pseudo gene
RPSAP69GeneProductENSG00000233487 (Ensembl) pseudo gene
S-palmitoyl-L-cysteine residue of a proteinMetabolite74151 (ChEBI)
SDHAP1GeneProductENSG00000185485 (Ensembl) pseudo gene
SENP5GeneProductENSG00000119231 (Ensembl)
SLC40A1GeneProductENSG00000138449 (Ensembl) Ferroportin
SLC51AGeneProductENSG00000163959 (Ensembl) OSTA, OSTalpha
SLC51BGeneProductENSG00000186198 (Ensembl) OSTB, OSTbeta
SMCO1GeneProductENSG00000214097 (Ensembl)
TCTEX1D2GeneProductENSG00000213123 (Ensembl)
TFGeneProductENSG00000091513 (Ensembl) Transferrin
TFRCGeneProductENSG00000072274 (Ensembl)
TM4SF19-AS1RnaENSG00000235897 (Ensembl) ncRNA
TM4SF19-TCTEX1D2RnaENSG00000273331 (Ensembl) ncRNA
TM4SF19GeneProductENSG00000145107 (Ensembl)
TNK2-AS1RnaENSG00000224614 (Ensembl) ncRNA
TNK2GeneProductENSG00000061938 (Ensembl) ACK1
Taurocholic acidMetabolite6675 (PubChem-compound)
UBXN7-AS1RnaENSG00000225822 (Ensembl) ncRNA
UBXN7GeneProductENSG00000163960 (Ensembl)
WDR34GeneProductENSG00000119333 (Ensembl)
WDR53GeneProductENSG00000185798 (Ensembl)
WDR60GeneProductENSG00000126870 (Ensembl)
WWOXGeneProductENSG00000186153 (Ensembl)
ZDHHC19GeneProductENSG00000163958 (Ensembl) Palmitoyltransferase
hsa-mir-4797RnaENSG00000265850 (Ensembl)
palmitoyl-CoA(4−)Metabolite57379 (ChEBI)

Annotated Interactions

SourceTargetTypeDatabase referenceComment
CTP4−CDP-choline(1−)mim-conversion18997 (Rhea)
CTP4−Diphosphate(3−)mim-conversion18997 (Rhea)
Choline phosphate(1−)CDP-choline(1−)mim-conversion18997 (Rhea)
Choline phosphate(1−)Diphosphate(3−)mim-conversion18997 (Rhea)
ZDHHC19mim-catalysis36683 (Rhea)
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