3q29 copy number variation syndrome (Homo sapiens)

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322032410, 217, 131222, 44292393145433119, 46402621225393086, 182138917, 33383815, 481511, 37322143419, 468, 11, 3727little information available:upregulated in regulatory macrophages during Leishmania infectionGlycosylphosphatidylinositol-mannosyltransferase 1phosphorylated stateChromosome 3:195,788,299Iron uptakeControls phosphatidylcholine synthesistranscriptionalsilencingspecific and selectivestimulation of TGFb1 inmicrogliaBile acid transportand uptakaunknown functionRNA genecentriole organizationProposed model of IFT dynein compositionRegulation of Iron uptakephosphorylationtargetsPalmitoylation35Choline phosphate(1−)HAMPATM signaling networkS-palmitoyl-L-cysteine residueof a proteinZNF76Nuclear cap-binding complexNCBP2AS2Taurocholic acidSLC40A1SMCO1RN7SL738PFe2+TCTEX1D2SENP5GRIA1TNK2-AS1UBXN7MAD2L1BPRNU6-646PSTAT5BMYCBP2TFNF2UBE2NJUNRNU6-910PPIGZDiphosphate(3−)NCBP2WDR53TM4SF19RNU6-42PL-serine residueCASP7RNU7-18PSLC51AZDHHC19Prostaglandin E2palmitoyl-CoA(4−)CoASIRT1LINC00885RPS29P3BRINP1TM4SF19-TCTEX1D2 O-phospho-L-serine(2−) residueRN7SL434PFe2+CEP19CTP4−STAT5AFBXW7MELTFhsa-mir-4797NRROSDLG1MYCRNF168L-cysteine residueof a proteinuH2BRNU4-89PDYNC2H1PIGXUBXN7-AS1TGFB1FNDC8HIF1ADYNC2LI1RNU2-11PPCYT1AMCRS1PIK3R3NCBP2-AS1Post-translational modification: synthesis of GPI-anchored proteinsMELTF-AS1RABL2BHFEPXNTFRCFGFR1OPADAM10DLG1-AS1PIGMTM4SF19-AS1LINC01063NCBP1RPSAP69PAK2FBXO45DigoxinCEP350RNF8Estrone sulfateWDR60FRAX1036SDHAP1RNU6-1279PSLC51BGenes related to primarycilium developmentCDP-choline(1−)Chromosome 3:197,033,296pseudo gene2130SLC51A151515242424WDR34TCTEX1D2DYNLT1TCTEX1D2DYNLT3DYNLRB1DYNLRB2DYNLL1DYNLL2DYNC2LI1DYNC2H1AKT1HIF1AUUubiquitinated stateRNF168FBXO45PIGXSTAT5AMYCSTAT5BPXNJUNNF2CASP7BRINP1SBRINP1SSUMOylated stateNCBP2


Description

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.

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Bibliography

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History

View all...
CompareRevisionActionTimeUserComment
135075view06:22, 5 August 2024EgonwUse an empty xref
135046view04:30, 2 August 2024EgonwFixed two identifiers ("ChEBI:" should be "CHEBI:")
135034view09:44, 1 August 2024EgonwMarked a CPX identifier as from the datasource "Complex Portal"
134669view15:10, 25 July 2024Ash iyerupdate node annotation
134668view15:07, 25 July 2024Ash iyeradded uH2H datanode within protein complex.
134622view11:05, 23 July 2024EweitzOntology Term : 'chromosomal duplication syndrome' added !
134621view11:04, 23 July 2024EweitzOntology Term : 'chromosomal deletion syndrome' added !
134620view11:03, 23 July 2024EweitzRefine legend
129011view12:44, 4 March 2024PklemmerRemoved linebreak from Nuclear cap-binding complex label
123416view11:17, 25 July 2022EgonwMade three pathways clickable
115773view13:39, 11 March 2021Fehrhartupdate to GRCh37
115768view12:42, 11 March 2021FehrhartModified description
115767view12:40, 11 March 2021Fehrhartupdated breakpoints
110951view16:49, 23 June 2020EgonwReplaced a secondary ChEBI identifier
110939view09:29, 23 June 2020Fehrhartwork in progress
110938view08:44, 23 June 2020Fehrhartwork in progress SENP5
110937view08:13, 23 June 2020Fehrhartwork in progress - PAK2
110927view13:42, 22 June 2020Fehrhartwork in progress - PIGX, CEP19
110907view13:40, 19 June 2020Fehrhartwork in progress NRROS
110899view12:04, 18 June 2020Fehrhartwork in progress - FBXO45
110898view11:50, 18 June 2020Fehrhartwork in progress RNF168 and SMCO1
110896view11:04, 18 June 2020Fehrhartwork in progress
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

DataNodes

View all...
NameTypeDatabase referenceComment
O-phospho-L-serine(2−) residueMetabolite83421 (ChEBI)
ADAM10GeneProductENSG00000137845 (Ensembl)
AKT1GeneProductENSG00000142208 (Ensembl)
ATM signaling networkPathwayWP3878 (WikiPathways)
BRINP1GeneProductENSG00000078725 (Ensembl) DBC1
CASP7GeneProductENSG00000165806 (Ensembl)
CDP-choline(1−)Metabolite58779 (ChEBI)
CEP19GeneProductENSG00000174007 (Ensembl)
CEP350GeneProductENSG00000135837 (Ensembl)
CTP4−Metabolite37563 (ChEBI)
Choline phosphate(1−)Metabolite295975 (ChEBI)
CoAMetabolite57287 (ChEBI)
DLG1-AS1RnaENSG00000227375 (Ensembl) ncRNA
DLG1GeneProductENSG00000075711 (Ensembl)
DYNC2H1GeneProductENSG00000187240 (Ensembl)
DYNC2LI1GeneProductENSG00000138036 (Ensembl)
DYNLL1GeneProductENSG00000088986 (Ensembl)
DYNLL2GeneProductENSG00000264364 (Ensembl)
DYNLRB1GeneProductENSG00000125971 (Ensembl)
DYNLRB2GeneProductENSG00000168589 (Ensembl)
DYNLT1GeneProductENSG00000146425 (Ensembl)
DYNLT3GeneProductENSG00000165169 (Ensembl)
DigoxinMetabolite2724385 (PubChem-compound)
Diphosphate(3−)Metabolite33019 (ChEBI)
Estrone sulfateMetabolite3001028 (PubChem-compound)
FBXO45GeneProductENSG00000174013 (Ensembl)
FBXW7GeneProductENSG00000109670 (Ensembl)
FGFR1OPGeneProductENSG00000213066 (Ensembl)
FNDC8GeneProductENSG00000073598 (Ensembl)
FRAX1036Metabolite71557891 (PubChem-compound)
Fe2+MetaboliteCHEBI:29033 (ChEBI)
GRIA1GeneProductENSG00000155511 (Ensembl) GluR1
Genes related to primary cilium developmentPathwayWP4536 (WikiPathways)
HAMPGeneProductENSG00000105697 (Ensembl)
HFEGeneProductENSG00000010704 (Ensembl)
HIF1AGeneProductENSG00000100644 (Ensembl)
JUNGeneProductENSG00000177606 (Ensembl)
L-cysteine residue of a proteinMetabolite29950 (ChEBI)
L-serine residueMetaboliteCHEBI:29999 (ChEBI)
LINC00885RnaENSG00000224652 (Ensembl) ncRNA
LINC01063RnaENSG00000232065 (Ensembl) ncRNA
MAD2L1BPGeneProductENSG00000124688 (Ensembl)
MCRS1GeneProductENSG00000187778 (Ensembl)
MELTF-AS1RnaENSG00000228109 (Ensembl) ncRNA
MELTFGeneProductENSG00000163975 (Ensembl)
MYCBP2GeneProductENSG00000005810 (Ensembl)
MYCGeneProductENSG00000136997 (Ensembl)
NCBP1GeneProductENSG00000136937 (Ensembl)
NCBP2-AS1RnaENSG00000225578 (Ensembl) ncRNA
NCBP2AS2RnaENSG00000270170 (Ensembl) ncRNA
NCBP2GeneProductENSG00000114503 (Ensembl)
NF2GeneProductENSG00000186575 (Ensembl) merlin
NRROSGeneProductENSG00000174004 (Ensembl) LRRC33
Nuclear cap-binding complexComplexCPX-1427 (EMBL) Complex Database (EMBL)
PAK2GeneProductENSG00000180370 (Ensembl)
PCYT1AGeneProductENSG00000161217 (Ensembl)
PIGMGeneProductENSG00000143315 (Ensembl)
PIGXGeneProductENSG00000163964 (Ensembl)
PIGZGeneProductENSG00000119227 (Ensembl)
PIK3R3GeneProductENSG00000117461 (Ensembl)
PXNGeneProductENSG00000089159 (Ensembl)
Post-translational modification: synthesis of GPI-anchored proteinsPathwayWP1887 (WikiPathways)
Prostaglandin E2Metabolite5280360 (PubChem-compound)
RABL2BGeneProductENSG00000079974 (Ensembl)
RN7SL434PGeneProductENSG00000241868 (Ensembl) pseudo
RN7SL738PGeneProductENSG00000243339 (Ensembl) pseudo
RNF168GeneProductENSG00000163961 (Ensembl)
RNF8GeneProductENSG00000112130 (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)
SIRT1GeneProductENSG00000096717 (Ensembl)
SLC40A1GeneProductENSG00000138449 (Ensembl) Ferroportin
SLC51AGeneProductENSG00000163959 (Ensembl) OSTA, OSTalpha
SLC51BGeneProductENSG00000186198 (Ensembl) OSTB, OSTbeta
SMCO1GeneProductENSG00000214097 (Ensembl)
STAT5AGeneProductENSG00000126561 (Ensembl)
STAT5BGeneProductENSG00000173757 (Ensembl)
TCTEX1D2GeneProductENSG00000213123 (Ensembl)
TFGeneProductENSG00000091513 (Ensembl) Transferrin
TFRCGeneProductENSG00000072274 (Ensembl)
TGFB1GeneProductENSG00000105329 (Ensembl)
TM4SF19-AS1RnaENSG00000235897 (Ensembl) ncRNA
TM4SF19-TCTEX1D2RnaENSG00000273331 (Ensembl) ncRNA
TM4SF19GeneProductENSG00000145107 (Ensembl)
TNK2-AS1RnaENSG00000224614 (Ensembl) ncRNA
Taurocholic acidMetabolite6675 (PubChem-compound)
UBE2NGeneProductENSG00000177889 (Ensembl)
UBXN7-AS1RnaENSG00000225822 (Ensembl) ncRNA
UBXN7GeneProductENSG00000163960 (Ensembl)
WDR34GeneProductENSG00000119333 (Ensembl)
WDR53GeneProductENSG00000185798 (Ensembl)
WDR60GeneProductENSG00000126870 (Ensembl)
ZDHHC19GeneProductENSG00000163958 (Ensembl) Palmitoyltransferase
ZNF76GeneProductENSG00000065029 (Ensembl)
hsa-mir-4797RnaENSG00000265850 (Ensembl)
palmitoyl-CoA(4−)Metabolite57379 (ChEBI)
uH2BGeneProductubiquitinated histone H2B - histone H2B is a gene family of about 23 genes

Annotated Interactions

View all...
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)
FNDC8MAD2L1BPmim-bindingEBI-25261866 (IntAct)
FNDC8MCRS1mim-bindingEBI-23791541 (IntAct)
FNDC8PIK3R3mim-bindingEBI-24039109 (IntAct)
FNDC8ZNF76mim-bindingEBI-23501218 (IntAct)
L-serine residue O-phospho-L-serine(2−) residuemim-conversion17989 (Rhea)
SMCO1FNDC8mim-bindingEBI-23405860 (IntAct)
ZDHHC19mim-catalysis36683 (Rhea)
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