3q29 copy number variation syndrome (Homo sapiens)

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404736, 394425, 233039321, 34822453511, 1712161527, 293238, 444826, 287465, 6, 2386433314391341911, 17220121, 25359731, 3741407101839transcriptionalsilencingBile acid transportand uptakalittle information available:upregulated in regulatory macrophages during Leishmania infectionProposed model of IFT dynein compositionIron uptakecentriole organizationChromosome 3:195,788,299RNA genePalmitoylationspecific and selectivestimulation of TGFb1 inmicrogliaunknown functionphosphorylationtargetsphosphorylated stateRegulation of Iron uptakeGlycosylphosphatidylinositol-mannosyltransferase 1catalysesphoshporylationon tyrosineControls phosphatidylcholine synthesis24DLG1MAD2L1BPATM signaling networkDLG1-AS1Genes related to primarycilium developmentKIF3AP1LINC01063TFRCApoptosis Fe2+RPSAP69HFEPIGMFe2+CoAHIF1AAKT1LINC00885palmitoyl-CoA(4−)MIR6829uH2BEstrone sulfateL-cysteine residueof a proteinSTAT5BSLC51AATMSTAT5ASMCO1Taurocholic acidCEP19PCYT1AADAM10RN7SL738PTM4SF19PIK3R3JUNCTP4−DYNC2H1MYCRNU7-18PDigoxinhsa-mir-4797RNU6-646PL-serine residueProstaglandin E2MELTF-AS1FBXW7PXNSLC51BWDR53NCBP2AS2Post-translational modification: synthesis of GPI-anchored proteinsUBXN7PAK2FRAX1036Nuclear cap-binding complexRPS29P3NCBP1HAMPCASP7TNK2BRINP1ERBB2SDHAP1UBE2NTM4SF19-AS1RABL2BFGFR1OPSENP5GRIA1LINC01983DNA Double Strand Break Response O-phospho-L-serine(2−) residueCEP350RNF168RNU6-910PMUC4SLC40A1RNU4-89PMCRS1SIRT1Diphosphate(3−)RNU6-42PPIGXMELTFRN7SL434PWDR60TCTEX1D2FNDC8GRB2PIGZDYNC2LI1RNU2-11PZNF76NCBP2-AS1RNF8ZDHHC19FBXO45NF2MYCBP2NCBP2WWOXCholine phosphate(1−)NRROSS-palmitoyl-L-cysteine residueof a proteinTFTNK2-AS1UBXN7-AS1RNU6-1279PTGFB1FYNCDP-choline(1−)ARTM4SF19-TCTEX1D2Chromosome 3:197,033,296AKT1ARWWOXFYNGRB2pseudo gene3932SLC51A1414144141WDR3441TCTEX1D2DYNLT1TCTEX1D2DYNLT3DYNLRB1DYNLRB2DYNLL1DYNLL2DYNC2LI1DYNC2H1AKT1HIF1AUUubiquitinated 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.

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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)
ARGeneProductENSG00000169083 (Ensembl) NR3C4
ATM signaling networkPathwayWP3878 (WikiPathways)
ATMGeneProductENSG00000149311 (Ensembl)
Apoptosis PathwayWP254 (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)
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)
FBXW7GeneProductENSG00000109670 (Ensembl)
FGFR1OPGeneProductENSG00000213066 (Ensembl)
FNDC8GeneProductENSG00000073598 (Ensembl)
FRAX1036Metabolite71557891 (PubChem-compound)
FYNGeneProductENSG00000010810 (Ensembl)
Fe2+MetaboliteCHEBI:29033 (ChEBI)
GRB2GeneProductENSG00000177885 (Ensembl)
GRIA1GeneProductENSG00000155511 (Ensembl) GluR1
Genes related to primary cilium developmentPathwayWP4536 (WikiPathways)
HAMPGeneProductENSG00000105697 (Ensembl)
HFEGeneProductENSG00000010704 (Ensembl)
HIF1AGeneProductENSG00000100644 (Ensembl)
JUNGeneProductENSG00000177606 (Ensembl)
KIF3AP1GeneProductENSG00000235836 (Ensembl) pseudo gene
L-cysteine residue of a proteinMetabolite29950 (ChEBI)
L-serine residueMetaboliteCHEBI:29999 (ChEBI)
LINC00885RnaENSG00000224652 (Ensembl) ncRNA
LINC01063RnaENSG00000232065 (Ensembl) ncRNA
LINC01983RnaENSG00000223783 (Ensembl) ncRNA
MAD2L1BPGeneProductENSG00000124688 (Ensembl)
MCRS1GeneProductENSG00000187778 (Ensembl)
MELTF-AS1RnaENSG00000228109 (Ensembl) ncRNA
MELTFGeneProductENSG00000163975 (Ensembl)
MIR6829RnaENSG00000276489 (Ensembl)
MUC4GeneProductENSG00000145113 (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
TNK2GeneProductENSG00000061938 (Ensembl) ACK1
Taurocholic acidMetabolite6675 (PubChem-compound)
UBE2NGeneProductENSG00000177889 (Ensembl)
UBXN7-AS1RnaENSG00000225822 (Ensembl) ncRNA
UBXN7GeneProductENSG00000163960 (Ensembl)
WDR34GeneProductENSG00000119333 (Ensembl)
WDR53GeneProductENSG00000185798 (Ensembl)
WDR60GeneProductENSG00000126870 (Ensembl)
WWOXGeneProductENSG00000186153 (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

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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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