1q21.1 copy number variation syndrome (Homo sapiens)

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12321, 2221, 23, 241415, 16201418, 1917tight junction proteinsAFDNF11ROCLNKIRREL1GJA3TJP3TJP1GJA1TJP211446possibly involved in head circumfence developmentn-oxidation of diet-derivedamino-trimethylaminesa subunitsChromosome 1:146,300,000pseudo genePFN1P8NBPF13PRNU1-151PPRKAG1PRKAA1PRKAA2PDIA3P1CCT8P1NOTCH2RNVU1-29PRKAG2RNVU1-25N,N-dimethylanilineNOTCH2NLAPRKAB2PPIAL4HFMO5N,N-dimethylaniline N-oxideRPL7AP15PRKAG3AMPPRKAB1HYDIN28RNA5SP536SEC22B4PRNVU1-8NBPF127Fatty acid b-oxidationNotch signalling(brain development)RNA geneneuroblastoma relatedunique in HomoPRKAB2b subunitsg subunitsAMPK5' AMP-activated protein kinase ADP12913102139935SchizophreniaBipolar disorderMajor depressive disorderChromosome 1: 147,800,000Helicase activity - involved inany DNA relaxation process required for DNA replication, repair and transcriptionEnamel formationCHD1LGJA8DNAOR13Z3PAMELXColon cancerGJA5ACP61-(9Z-octadecenoyl)-sn-glycero-3-phosphateWNT signaling pathwayRN7SL261PLINC00624an alcoholPhosphateCTNNB1OR13Z2P1-(9Z-octadecenoyl)-sn-glycerolHeart developmentBase Excision RepairPYGO1OR13Z1PBCL9phosphate monoestersBCL9PYGO2PYGO1BCL9PYGO2Phosphate3gap junction proteins


1q21.1 copy number variation (deletion or duplication) syndromes are known for a highly variable phenotype especially concerning 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. Li J, Zhou G, Ji W, Feng G, Zhao Q, Liu J, Li T, Li Y, Chen P, Zeng Z, Wang T, Hu Z, Zheng L, Wang Y, Shen Y, He L, Shi Y; ''Common variants in the BCL9 gene conferring risk of schizophrenia.''; Arch Gen Psychiatry, 2011 PubMed Europe PMC Scholia
  2. Hiroyama M, Takenawa T; ''Isolation of a cDNA encoding human lysophosphatidic acid phosphatase that is involved in the regulation of mitochondrial lipid biosynthesis.''; J Biol Chem, 1999 PubMed Europe PMC Scholia
  3. Fanning AS, Jameson BJ, Jesaitis LA, Anderson JM; ''The tight junction protein ZO-1 establishes a link between the transmembrane protein occludin and the actin cytoskeleton.''; J Biol Chem, 1998 PubMed Europe PMC Scholia
  4. Liu G, Kaw B, Kurfis J, Rahmanuddin S, Kanwar YS, Chugh SS; ''Neph1 and nephrin interaction in the slit diaphragm is an important determinant of glomerular permeability.''; J Clin Invest, 2003 PubMed Europe PMC Scholia
  5. Ebnet K, Aurrand-Lions M, Kuhn A, Kiefer F, Butz S, Zander K, Meyer zu Brickwedde MK, Suzuki A, Imhof BA, Vestweber D; ''The junctional adhesion molecule (JAM) family members JAM-2 and JAM-3 associate with the cell polarity protein PAR-3: a possible role for JAMs in endothelial cell polarity.''; J Cell Sci, 2003 PubMed Europe PMC Scholia
  6. Flaus A, Martin DM, Barton GJ, Owen-Hughes T; ''Identification of multiple distinct Snf2 subfamilies with conserved structural motifs.''; Nucleic Acids Res, 2006 PubMed Europe PMC Scholia
  7. Rao RK, Basuroy S, Rao VU, Karnaky KJ Jr, Gupta A; ''Tyrosine phosphorylation and dissociation of occludin-ZO-1 and E-cadherin-beta-catenin complexes from the cytoskeleton by oxidative stress.''; Biochem J, 2002 PubMed Europe PMC Scholia
  8. Itoh M, Morita K, Tsukita S; ''Characterization of ZO-2 as a MAGUK family member associated with tight as well as adherens junctions with a binding affinity to occludin and alpha catenin.''; J Biol Chem, 1999 PubMed Europe PMC Scholia
  9. Nielsen PA, Baruch A, Shestopalov VI, Giepmans BN, Dunia I, Benedetti EL, Kumar NM; ''Lens connexins alpha3Cx46 and alpha8Cx50 interact with zonula occludens protein-1 (ZO-1).''; Mol Biol Cell, 2003 PubMed Europe PMC Scholia
  10. Li J, Dong Y, Lü X, Wang L, Peng W, Zhang XC, Rao Z; ''Crystal structures and biochemical studies of human lysophosphatidic acid phosphatase type 6.''; Protein Cell, 2013 PubMed Europe PMC Scholia
  11. Dougherty ML, Nuttle X, Penn O, Nelson BJ, Huddleston J, Baker C, Harshman L, Duyzend MH, Ventura M, Antonacci F, Sandstrom R, Dennis MY, Eichler EE; ''The birth of a human-specific neural gene by incomplete duplication and gene fusion.''; Genome Biol, 2017 PubMed Europe PMC Scholia
  12. Cantù C, Felker A, Zimmerli D, Prummel KD, Cabello EM, Chiavacci E, Méndez-Acevedo KM, Kirchgeorg L, Burger S, Ripoll J, Valenta T, Hausmann G, Vilain N, Aguet M, Burger A, Panáková D, Basler K, Mosimann C; ''Mutations inBcl9andPygogenes cause congenital heart defects by tissue-specific perturbation of Wnt/β-catenin signaling.''; Genes Dev, 2018 PubMed Europe PMC Scholia
  13. Huber TB, Schmidts M, Gerke P, Schermer B, Zahn A, Hartleben B, Sellin L, Walz G, Benzing T; ''The carboxyl terminus of Neph family members binds to the PDZ domain protein zonula occludens-1.''; J Biol Chem, 2003 PubMed Europe PMC Scholia
  14. Bernier R, Steinman KJ, Reilly B, Wallace AS, Sherr EH, Pojman N, Mefford HC, Gerdts J, Earl R, Hanson E, Goin-Kochel RP, Berry L, Kanne S, Snyder LG, Spence S, Ramocki MB, Evans DW, Spiro JE, Martin CL, Ledbetter DH, Chung WK; ''Clinical phenotype of the recurrent 1q21.1 copy-number variant.''; Genet Med, 2016 PubMed Europe PMC Scholia
  15. Vandepoele K, Van Roy N, Staes K, Speleman F, van Roy F; ''A novel gene family NBPF: intricate structure generated by gene duplications during primate evolution.''; Mol Biol Evol, 2005 PubMed Europe PMC Scholia
  16. Fiddes IT, Lodewijk GA, Mooring M, Bosworth CM, Ewing AD, Mantalas GL, Novak AM, van den Bout A, Bishara A, Rosenkrantz JL, Lorig-Roach R, Field AR, Haeussler M, Russo L, Bhaduri A, Nowakowski TJ, Pollen AA, Dougherty ML, Nuttle X, Addor MC, Zwolinski S, Katzman S, Kriegstein A, Eichler EE, Salama SR, Jacobs FMJ, Haussler D; ''Human-Specific NOTCH2NL Genes Affect Notch Signaling and Cortical Neurogenesis.''; Cell, 2018 PubMed Europe PMC Scholia
  17. Giepmans BN, Moolenaar WH; ''The gap junction protein connexin43 interacts with the second PDZ domain of the zona occludens-1 protein.''; Curr Biol, 1998 PubMed Europe PMC Scholia
  18. Moor AE, Anderle P, Cantù C, Rodriguez P, Wiedemann N, Baruthio F, Deka J, André S, Valenta T, Moor MB, Győrffy B, Barras D, Delorenzi M, Basler K, Aguet M; ''BCL9/9L-β-catenin Signaling is Associated With Poor Outcome in Colorectal Cancer.''; EBioMedicine, 2015 PubMed Europe PMC Scholia
  19. Wittchen ES, Haskins J, Stevenson BR; ''Protein interactions at the tight junction. Actin has multiple binding partners, and ZO-1 forms independent complexes with ZO-2 and ZO-3.''; J Biol Chem, 1999 PubMed Europe PMC Scholia
  20. Cantù C, Pagella P, Shajiei TD, Zimmerli D, Valenta T, Hausmann G, Basler K, Mitsiadis TA; ''A cytoplasmic role of Wnt/β-catenin transcriptional cofactors Bcl9, Bcl9l, and Pygopus in tooth enamel formation.''; Sci Signal, 2017 PubMed Europe PMC Scholia
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  23. Ebnet K, Schulz CU, Meyer Zu Brickwedde MK, Pendl GG, Vestweber D; ''Junctional adhesion molecule interacts with the PDZ domain-containing proteins AF-6 and ZO-1.''; J Biol Chem, 2000 PubMed Europe PMC Scholia
  24. Stapleton D, Mitchelhill KI, Gao G, Widmer J, Michell BJ, Teh T, House CM, Fernandez CS, Cox T, Witters LA, Kemp BE; ''Mammalian AMP-activated protein kinase subfamily.''; J Biol Chem, 1996 PubMed Europe PMC Scholia


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113763view15:21, 19 November 2020DeSlUpdated old HMDB IDs (second try)
113762view15:20, 19 November 2020DeSlUpdated old HMDB IDs
113701view08:30, 17 November 2020Fehrhartformat update for pathway node
110320view22:28, 3 May 2020Marvin M2Ontology Term : 'chromosome 1q21.1 duplication syndrome' added !
110319view22:28, 3 May 2020Marvin M2Ontology Term : 'chromosome 1q21.1 deletion syndrome' added !
110318view22:27, 3 May 2020Marvin M2Ontology Term : 'chromosomal disease' added !
110258view15:21, 30 April 2020EgonwReplaced secondary ChEBI identifiers with a primary identifiers.
110216view13:42, 24 April 2020Fehrhartfinalized addition of interactions
110191view15:13, 23 April 2020Fehrhartwork in progress
110190view15:06, 23 April 2020FehrhartOntology Term : 'bipolar disorder' added !
110189view15:05, 23 April 2020FehrhartOntology Term : 'major depressive disorder' added !
110188view15:05, 23 April 2020FehrhartOntology Term : 'schizophrenia' added !
110187view15:04, 23 April 2020FehrhartOntology Term : 'inborn error of metabolism pathway' added !
110186view15:04, 23 April 2020FehrhartOntology Term : 'congenital disease pathway' added !
110183view15:03, 23 April 2020Fehrhartwork in progress
110168view07:46, 23 April 2020FehrhartModified description
110167view07:46, 23 April 2020FehrhartModified description
110166view07:45, 23 April 2020FehrhartModified title
110164view15:46, 22 April 2020Fehrhartwork in progress
110163view15:21, 22 April 2020Fehrhartaddition of downstream known functions
110146view06:14, 21 April 2020FehrhartNew pathway

External references


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NameTypeDatabase referenceComment
1-(9Z-octadecenoyl)-sn-glycero-3-phosphateMetaboliteCHEBI:62837 (ChEBI)
1-(9Z-octadecenoyl)-sn-glycerolMetaboliteCHEBI:75757 (ChEBI)
ACP6GeneProductENSG00000162836 (Ensembl)
ADPMetaboliteCHEBI:16761 (ChEBI)
AFDNGeneProductENSG00000130396 (Ensembl)
AMELXGeneProductENSG00000125363 (Ensembl)
AMPMetaboliteCHEBI:16027 (ChEBI)
BCL9GeneProductENSG00000116128 (Ensembl)
Base Excision RepairPathwayWP1980 (WikiPathways)
CCT8P1GeneProductENSG00000226015 (Ensembl) pseudo gene
CHD1LGeneProductENSG00000131778 (Ensembl)
CTNNB1GeneProductENSG00000168036 (Ensembl)
Colon cancerPathwayWP4239 (WikiPathways)
DNAMetaboliteCHEBI:16991 (ChEBI)
F11RGeneProductENSG00000158769 (Ensembl) CD321
FMO5GeneProductENSG00000131781 (Ensembl)
Fatty acid b-oxidationPathwayWP368 (WikiPathways)
GJA1GeneProductENSG00000152661 (Ensembl)
GJA3GeneProductENSG00000121743 (Ensembl)
GJA5GeneProductENSG00000265107 (Ensembl) connexin 40 (Cx40)
GJA8GeneProductENSG00000121634 (Ensembl) connexin 50
HYDIN2GeneProductENSG00000276975 (Ensembl) origin known, but not function
Heart developmentPathwayWP1591 (WikiPathways)
KIRREL1GeneProductENSG00000183853 (Ensembl)
LINC00624RnaENSG00000278811 (Ensembl) ncRNA
N,N-dimethylaniline N-oxideMetaboliteCHEBI:17735 (ChEBI)
N,N-dimethylanilineMetaboliteCHEBI:16269 (ChEBI)
NBPF12GeneProductENSG00000268043 (Ensembl)
NBPF13PGeneProductENSG00000227242 (Ensembl) pseudo gene
NOTCH2GeneProductENSG00000134250 (Ensembl)
NOTCH2NLAGeneProductENSG00000264343 (Ensembl) N2N, notch 2 N-terminal like, notch 2 N-terminal like A, NOTCH2NL
Notch signalling (brain development)PathwayWP268 (WikiPathways)
OCLNGeneProductENSG00000197822 (Ensembl)
OR13Z1PGeneProductENSG00000226653 (Ensembl) pseudo gene
OR13Z2PGeneProductENSG00000272443 (Ensembl) pseudo gene
OR13Z3PGeneProductENSG00000272480 (Ensembl) pseudo gene
PDIA3P1GeneProductENSG00000180867 (Ensembl) pseudo gene
PFN1P8GeneProductENSG00000244371 (Ensembl) pseudo gene
PPIAL4HGeneProductENSG00000270339 (Ensembl) a peptidylprolyl isomerase - no concrete function known
PRKAA1GeneProductENSG00000132356 (Ensembl)
PRKAA2GeneProductENSG00000162409 (Ensembl)
PRKAB1GeneProductENSG00000111725 (Ensembl)
PRKAB2GeneProductENSG00000131791 (Ensembl) regulatory subunit
PRKAG1GeneProductENSG00000181929 (Ensembl)
PRKAG2GeneProductENSG00000106617 (Ensembl)
PRKAG3GeneProductENSG00000115592 (Ensembl)
PYGO1GeneProductENSG00000171016 (Ensembl)
PYGO2GeneProductENSG00000163348 (Ensembl)
PhosphateMetaboliteHMDB01429 (HMDB)
RN7SL261PGeneProductENSG00000277762 (Ensembl) pseudo gene
RNA5SP536GeneProductENSG00000274408 (Ensembl) pseudogene
RNU1-151PGeneProductENSG00000201142 (Ensembl) pseudo gene
RNVU1-25GeneProductENSG00000274428 (Ensembl) snRNA
RNVU1-29RnaENSG00000273768 (Ensembl) snRNA
RNVU1-8RnaENSG00000286172 (Ensembl) snRNA
RPL7AP15GeneProductENSG00000236806 (Ensembl) pseudo gene
SEC22B4PGeneProductENSG00000277406 (Ensembl) pseudogene
TJP1GeneProductENSG00000104067 (Ensembl)
TJP2GeneProductENSG00000119139 (Ensembl)
TJP3GeneProductENSG00000105289 (Ensembl)
WNT signaling pathwayPathwayWP428 (WikiPathways)
an alcoholMetaboliteCHEBI:30879 (ChEBI)
phosphate monoestersMetaboliteCHEBI:7794 (ChEBI)

Annotated Interactions

SourceTargetTypeDatabase referenceComment
1-(9Z-octadecenoyl)-sn-glycero-3-phosphate1-(9Z-octadecenoyl)-sn-glycerolmim-conversion39835 (Rhea)
1-(9Z-octadecenoyl)-sn-glycero-3-phosphatePhosphatemim-conversion39835 (Rhea)
N,N-dimethylanilineN,N-dimethylaniline N-oxidemim-conversion24468 (Rhea)
phosphate monoestersPhosphatemim-conversion15017 (Rhea)
phosphate monoestersan alcoholmim-conversion15017 (Rhea)
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