Smith-Magenis and Potocki-Lupski syndrome copy number variation (Homo sapiens)

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IRF8PITPK1PJUNPTFE3TFEBPPPTENCRY1P747940279514036, 41102643330, 539578783452805418, 453319, 72714019, 727466917930912236, 41338937546466859, 8568, 9259, 85149270779342, 824659, 85211269443120, 473889216123, 42, 49, 82758956, 81, 8320, 47556923, 42, 495514, 3238, 816135, 76173946, 6761, 64371748, 50699359, 8520, 4714, 32926528696056, 839757, 843994411, 1339573937, 486, 7351844518, 4351, 585791686, 9415241, 1350, 9048737, 4811, 946324735162863937, 48Endosome inactive state specific functionunknownMitochondrial fissionhomeostatic functions such as feeding, sleeping and temperaturebut also role in inflammation and pain mitochondrial fusionregulation of cytoskeleton regulation of endothelial senescencetraffics and delivers critical molecules required for stereocilia development Initiation of chromosomalDNA replication Axonogenesismitochondrial fission assembly of the axoneme during spermiogenesis late meiotic and haploid phases of spermatogenesisRNA stability and cellular stress responseregulation of epithelial cell polarityGluconeogenesisMidbrain dopaminergic neurogenesisdecatenation and segregation of mtDNA synthesis of methionine, thymidylate, and purines in the cytoplasm.plasma cell differentiation5, 51Protects mitochondrial DNA replication from excess dTTPincrease and stabilization of actin filaments 57, 84cytochrome C releasediacylglycerolRRAGALDHAAPPCREB1MYCMIGA1MTORC1STAT3MTOR signalling Core mediatorcomplexAMPK complexTP53FE65Thymine PDMEAutophagysynaptogenesis and neurogenesisnoncanonical NF-kB pathwayPiRNA biogenesisFHOD1Phosphatidylcholine catabolismPEYAP1UBP8TFEBcell cycleMicrotubule cytoskeleton regulationcardiolipinphosphatidate RNA polymerase II E3 ubiquitin ligasesignalling pathwayMLST8PRKAA1lipin familyglycolysisUracilAP-1 familyTFE3PCARM1C9orf72-SMCR8MAEADRC1PRKNUbC9ORF72NR1H3TLR4Fatty acid synthesis Intraflagellartransport complex BRAB8AGDP MLST8RNF41 NFKB1IFT81PCK1ROSNR1H2TNF-α signalingpathway TOLLIPmRNA WDR41LRRC48RO60MYH2CLTCTNFAutophagyGRIP1PARD6BMPRIPATP synthasecomplexMitophagyPAR cellpolarity complexNF-κB P50/P65CLTASREB2HBP1UbMYO16ARG2PEMTSMCR8DRP1GDI2FOXA1NT5MFNIP2TNFRSF13B29cortisolCOPS3MAP3K14Zinc 2+ ATPAF2MYPT1PHomologous recombinationRAI1BAFFPRDM1GID4ALKBH5DRG2BAX73MIEF2CLEC16ACFL2PTOP3AFLIICRY1RASD1BCL2L11CRY2one-carbon compoundTOM1L2PER1CRY2PPER1PFLCNCOP9signalosomeROCK162LIMK1P6, 73BMLL-serineTNFSF13RMI2MYO15ARMI1ApoptosisTOP3AApoptosisBMAL1melatoninRhoAglycineMagnesium 2+SREBF1BTR complexMED9CDK1 BIRC2BCL6LLGL1CFL2pyridoxal 5'-phosphate(2-)CLOCKSHMT1PRKNSMCR8RAB8AGTP RAB39BGTPRAB39BGDPULK1RB1CC1ATG13ATG101ULK1 complexRPTORMTORMTORC127MYD8832MYD88RELA14IL1BPRKCIPARD3RAB10RAB10mRNA MeY RNADRC3CCDC65GAS8TCTE1FBXL13DRC7EFCAB2IQCGIQCDIQCA146IFT7446IFT22IFT22IFT81IFT74TTC26IFT46IFT52IFT172IFT80IFT88TTC30BIFT57CLUAP1IFT20IFT27IFT25TRAF3IP14646TOM1L2CLTCCLTCCLTACLTB2576MIR33BG6PC1FOXA2HES6FERD3LSMCR5MKLN1ARMC8WDR26RMND5ARANBP9GID4HBP1SMCR2UracilPThymine RP11-45M22.4PLD6MIGA2PRKAG2PRKAB1WWTR1ETV5PPP1R14ATNFRSF13BTNFRSF13BFLCNFLCNFNIP1RPTORMTORCOPS7ACOPS5COPS6COPS8COPS3COPS2COPS4GPS1Zinc 2+ TP53PJUNITPK118, 45IRF845MED9PMMEphosphatidylcholine30, 5330, 5330, 5330, 53CREB30, 53PGene ProductData node for a RNA gene or its RNA transcriptMetabolitePathwayData node for a protein coding gene or its proteinData node for a pseudogene Data node for a metabolite Data node for a pathwayPMIM-necessary stimulation of an enzyme or a gene that is necessary for activation or expressionMIM-binding of compound to another MIM-conversion of a compound to another MIM-stimulation of an enzyme or a gene leading to activation or expressionMIM-catalysis of a compound by an enzyme MIM-inhibition of a compound's function or a process MIM-transcription of a gene MeComplex Complex Phosphorylated protein UbUbiquitinated protein Methylated protein or geneLegend Gene ProductGene ProductChr17: 18,280,000Chr17: 16,812,771


Description

The Smith-Magenis syndrome, is the result from a deletion of chr17:chr17:16,82-18,28, while the Potocki-Lupski syndrome is the result of a duplication of this area.

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  94. Ono M, Ando H, Daikoku T, Fujiwara T, Mieda M, Mizumoto Y, Iizuka T, Kagami K, Hosono T, Nomura S, Toyoda N, Sekizuka-Kagami N, Maida Y, Kuji N, Nishi H, Fujiwara H; ''The Circadian Clock, Nutritional Signals and Reproduction: A Close Relationship.''; Int J Mol Sci, 2023 PubMed Europe PMC Scholia
  95. Huang H, Gao Q, Peng X, Choi SY, Sarma K, Ren H, Morris AJ, Frohman MA; ''piRNA-associated germline nuage formation and spermatogenesis require MitoPLD profusogenic mitochondrial-surface lipid signaling.''; Dev Cell, 2011 PubMed Europe PMC Scholia

History

View all...
CompareRevisionActionTimeUserComment
134446view23:53, 21 July 2024EweitzOntology Term : 'Potocki-Lupski syndrome' added !
134445view23:52, 21 July 2024EweitzOntology Term : 'Smith-Magenis syndrome' added !
134396view19:45, 21 July 2024EweitzRemove template comments
127624view20:29, 8 November 2023LarsgwRemove duplicate references
127450view18:30, 3 October 2023Khanspersconverted interactions in legend to graphical lines
127076view16:37, 27 July 2023Fehrhartcorrection and update in progress
127075view16:17, 27 July 2023FehrhartOntology Term : 'disease pathway' added !
127004view14:06, 17 July 2023Ash iyerData nodes annotation updated.
126969view19:06, 9 July 2023Ninagerrekens
126924view14:23, 6 July 2023EgonwReplaced SwissProt with TrEMBL
126891view09:39, 30 June 2023EgonwAdding some missing reference data
126890view09:38, 30 June 2023Egonw'Complex Portal' data source
126686view22:31, 12 June 2023NinagerrekensNew pathway

External references

DataNodes

View all...
NameTypeDatabase referenceComment
Protein
ALKBH5GeneProductENSG00000091542 (Ensembl)
AMPK complexComplexCPX-5786 (Complex Portal)
AP-1 familyProteinIPR000837 (Uniprot-TrEMBL)
APPProteinP05067 (Uniprot-TrEMBL)
ARG2ProteinP78540 (Uniprot-TrEMBL)
ARMC8ProteinQ8IUR7 (Uniprot-TrEMBL)
ATG101ProteinQ9BSB4 (Uniprot-TrEMBL)
ATG13ProteinO75143 (Uniprot-TrEMBL)
ATP synthase complexComplexCPX-6151 (Complex Portal)
ATPAF2GeneProductENSG00000171953 (Ensembl)
ApoptosisPathwayWP254 (WikiPathways)
AutophagyPathwayWP4923 (WikiPathways)
BAFFProteinQ8JHJ4 (Uniprot-TrEMBL) Blys is a synonym
BAXProteinQ07812 (Uniprot-TrEMBL)
BCL2L11ProteinO43521 (Uniprot-TrEMBL) also known as BCL2L11
BCL6ProteinA0A0C4DH53 (Uniprot-TrEMBL)
BIRC2ProteinE9PI77 (Uniprot-TrEMBL) cIAP-1 is a synonym for BIRC2
BMAL1ProteinO00327 (Uniprot-TrEMBL)
BMLProteinP54132 (Uniprot-TrEMBL)
BTR complexComplexCPX-3301 (Complex Portal)
C9ORF72ProteinQ96LT7 (Uniprot-TrEMBL)
C9orf72-SMCR8ComplexCPX-3961 (Complex Portal)
CARM1ProteinQ86X55 (Uniprot-TrEMBL)
CCDC65ProteinQ8IXS2 (Uniprot-TrEMBL)
CDK1 ProteinP06493 (Uniprot-TrEMBL)
CFL2ProteinQ9Y281 (Uniprot-TrEMBL)
CLEC16AProteinQ2KHT3 (Uniprot-TrEMBL)
CLOCKProteinO15516 (Uniprot-TrEMBL)
CLTAProteinP09496 (Uniprot-TrEMBL) Clathrin a
CLTBProteinP09497 (Uniprot-TrEMBL) Clathrin a
CLTCProteinQ00610 (Uniprot-TrEMBL)
CLUAP1ProteinQ96AJ1 (Uniprot-TrEMBL)
COP9 signalosomeComplexCPX-1870 (Complex Portal)
COPS2ProteinP61201 (Uniprot-TrEMBL)
COPS3GeneProductENSG00000141030 (Ensembl)
COPS3ProteinQ9UNS2 (Uniprot-TrEMBL)
COPS4ProteinQ9BT78 (Uniprot-TrEMBL)
COPS5ProteinQ92905 (Uniprot-TrEMBL)
COPS6ProteinQ7L5N1 (Uniprot-TrEMBL)
COPS7AProteinQ9UBW8 (Uniprot-TrEMBL)
COPS8ProteinQ99627 (Uniprot-TrEMBL)
CREB1ProteinENSG00000118260 (Ensembl)
CREBProteinENSG00000118260 (Ensembl)
CRY1Protein1407 (Entrez Gene)
CRY1ProteinQ16526 (Uniprot-TrEMBL)
CRY2Protein1408 (Entrez Gene)
CRY2ProteinQ49AN0 (Uniprot-TrEMBL)
Core mediator complexComplexCPX-3227 (Complex Portal)
DRC1ProteinQ96MC2 (Uniprot-TrEMBL)
DRC3ProteinQ9H069 (Uniprot-TrEMBL) Is protein of LRRC48
DRC7ProteinQ8IY82 (Uniprot-TrEMBL)
DRG2GeneProductENSG00000108591 (Ensembl)
DRP1ProteinO43583 (Uniprot-TrEMBL)
E3 ubiquitin ligase signalling pathwayPathwayWP4055 (WikiPathways)
EFCAB2ProteinQ5VUJ9 (Uniprot-TrEMBL)
ETV5ProteinP41161 (Uniprot-TrEMBL)
FBXL13ProteinQ8NEE6 (Uniprot-TrEMBL)
FE65ProteinO00213 (Uniprot-TrEMBL)
FERD3LProteinQ96RJ6 (Uniprot-TrEMBL)
FHOD1ProteinQ9Y613 (Uniprot-TrEMBL)
FLCNGeneProductENSG00000154803 (Ensembl)
FLIIGeneProductENSG00000177731 (Ensembl)
FNIP1ProteinQ8TF40 (Uniprot-TrEMBL)
FNIP2ProteinQ9P278 (Uniprot-TrEMBL)
FOXA1ProteinP55317 (Uniprot-TrEMBL)
FOXA2ProteinQ9Y261 (Uniprot-TrEMBL)
Fatty acid synthesis PathwayWP357 (WikiPathways)
G6PC1ProteinP35575 (Uniprot-TrEMBL)
GAS8ProteinO95995 (Uniprot-TrEMBL)
GDI2ProteinP50395 (Uniprot-TrEMBL)
GID4GeneProductENSG00000141034 (Ensembl)
GID4ProteinQ8IVV7 (Uniprot-TrEMBL)
GPS1ProteinQ13098 (Uniprot-TrEMBL)
GRIP1ProteinQ9Y3R0 (Uniprot-TrEMBL)
HBP1ProteinO60381 (Uniprot-TrEMBL)
HES6ProteinQ96HZ4 (Uniprot-TrEMBL)
Homologous recombinationPathwayWP5096 (WikiPathways)
IFT172ProteinQ9UG01 (Uniprot-TrEMBL)
IFT20ProteinQ8IY31 (Uniprot-TrEMBL)
IFT22ProteinQ9H7X7 (Uniprot-TrEMBL)
IFT25ProteinQ9Y547 (Uniprot-TrEMBL)
IFT27ProteinQ9BW83 (Uniprot-TrEMBL)
IFT46ProteinQ9NQC8 (Uniprot-TrEMBL)
IFT52ProteinQ9Y366 (Uniprot-TrEMBL)
IFT57ProteinQ9NWB7 (Uniprot-TrEMBL)
IFT74ProteinQ96LB3 (Uniprot-TrEMBL)
IFT80ProteinQ9P2H3 (Uniprot-TrEMBL)
IFT81ProteinQ8WYA0 (Uniprot-TrEMBL)
IFT88ProteinQ13099 (Uniprot-TrEMBL)
IL1BProteinP01584 (Uniprot-TrEMBL) proinflammatory cytokine
IQCA1ProteinQ86XH1 (Uniprot-TrEMBL)
IQCDProteinQ96DY2 (Uniprot-TrEMBL)
IQCGProteinQ9H095 (Uniprot-TrEMBL)
IRF8ProteinQ02556 (Uniprot-TrEMBL)
ITPK1ProteinQ13572 (Uniprot-TrEMBL)
Intraflagellar transport complex BComplexCPX-5022 (Complex Portal)
JUNProteinP05412 (Uniprot-TrEMBL)
L-serineMetabolite33384 (ChEBI)
LDHAProteinP00338 (Uniprot-TrEMBL)
LIMK1ProteinP53667 (Uniprot-TrEMBL)
LLGL1GeneProductENSG00000131899 (Ensembl)
LRRC48GeneProductENSG00000171962 (Ensembl)
MAEAProteinQ7L5Y9 (Uniprot-TrEMBL)
MAP3K14ProteinQ99558 (Uniprot-TrEMBL) NIK is short for NF-κB-inducing kinase
MED9GeneProductENSG00000141026 (Ensembl)
MIEF2GeneProductENSG00000177427 (Ensembl) outer mitochondrial membrane
MIGA1ProteinQ8NAN2 (Uniprot-TrEMBL)
MIGA2ProteinQ7L4E1 (Uniprot-TrEMBL)
MIR33BGeneProductENSG00000207839 (Ensembl) MiRNA
MKLN1ProteinQ9UL63 (Uniprot-TrEMBL)
MLST8ProteinQ9BVC4 (Uniprot-TrEMBL)
MPRIPGeneProductENSG00000133030 (Ensembl) KIAA0864, M-RIP, MRIP, RHOIP3, RIP3, p116Rip are other names for MPRIP
MTOR signalling PathwayWP3318 (WikiPathways)
MTORC1ComplexCPX-503 (Complex Portal)
MTORProteinP42345 (Uniprot-TrEMBL)
MYCProteinP01106 (Uniprot-TrEMBL)
MYD88ProteinQ99836 (Uniprot-TrEMBL)
MYH2ProteinQ9UKX2 (Uniprot-TrEMBL)
MYO15AGeneProductENSG00000091536 (Ensembl) expressed in hair cells of the inner ear
MYO16ProteinQ9Y6X6 (Uniprot-TrEMBL)
MYPT1ProteinO14974 (Uniprot-TrEMBL)
Magnesium 2+Metabolite18420 (ChEBI)
MetaboliteMetabolite
Microtubule cytoskeleton regulationPathwayWP2038 (WikiPathways)
MitophagyPathwayWP3549 (WikiPathways)
NF-κB P50/P65ComplexCPX-5828 (Complex Portal)
NFKB1ProteinP19838 (Uniprot-TrEMBL)
NR1H2ProteinP55055 (Uniprot-TrEMBL)
NR1H3ProteinQ13133 (Uniprot-TrEMBL)
NT5MGeneProductENSG00000205309 (Ensembl)
PAR cell polarity complexComplexCPX-6193 (Complex Portal)
PARD3ProteinQ8TEW0 (Uniprot-TrEMBL)
PARD6BProteinQ9BYG5 (Uniprot-TrEMBL)
PCK1ProteinP35558 (Uniprot-TrEMBL)
PDMEMetabolite64572 (ChEBI)
PEMetabolite16038 (ChEBI)
PEMTGeneProductENSG00000133027 (Ensembl)
PER1Protein5187 (Entrez Gene)
PER1ProteinO15534 (Uniprot-TrEMBL)
PLD6GeneProductENSG00000179598 (Ensembl) ZUC and MitoPLD are different names for PLD6
PMMEMetabolite64573 (ChEBI)
PPP1R14AProteinQ96A00 (Uniprot-TrEMBL)
PRDM1ProteinO75626 (Uniprot-TrEMBL)
PRKAA1ProteinQ13131 (Uniprot-TrEMBL)
PRKAB1ProteinQ9Y478 (Uniprot-TrEMBL)
PRKAG2ProteinQ9UGJ0 (Uniprot-TrEMBL)
PRKCIProteinP41743 (Uniprot-TrEMBL)
PRKNProteinO60260 (Uniprot-TrEMBL)
PTENProteinP60484 (Uniprot-TrEMBL)
PathwayPathway
Phosphatidylcholine catabolismPathwayWP4195 (WikiPathways)
PiRNA biogenesisPathwayR-HSA-5601884 (Reactome)
RAB10ProteinP61026 (Uniprot-TrEMBL)
RAB39BProteinQ96DA2 (Uniprot-TrEMBL)
RAB8AProteinP61006 (Uniprot-TrEMBL)
RAI1GeneProductENSG00000108557 (Ensembl)
RANBP9ProteinQ96S59 (Uniprot-TrEMBL)
RASD1GeneProductENSG00000108551 (Ensembl)
RB1CC1ProteinQ8TDY2 (Uniprot-TrEMBL) FIP200
RELAProteinQ04206 (Uniprot-TrEMBL)
RMI1ProteinQ9H9A7 (Uniprot-TrEMBL)
RMI2ProteinQ96E14 (Uniprot-TrEMBL)
RMND5AProteinQ9H871 (Uniprot-TrEMBL)
RNA polymerase II PathwayWP4933 (WikiPathways)
RNF41 ProteinQ9H4P4 (Uniprot-TrEMBL)
RO60ProteinP10155 (Ensembl)
ROCK1ProteinQ13464 (Uniprot-TrEMBL)
ROSMetabolite26523 (ChEBI)
RP11-45M22.4GeneProductENSG00000264187 (Ensembl)
RPTORProteinQ8N122 (Uniprot-TrEMBL)
RRAGAProteinQ7L523 (Uniprot-TrEMBL)
RhoAProteinP61586 (Uniprot-TrEMBL)
SHMT1GeneProductENSG00000176974 (Ensembl)
SMCR2GeneProductENSG00000223979 (Ensembl) LincRNA
SMCR5GeneProductENSG00000226746 (Ensembl) antisense
SMCR8GeneProductENSG00000176994 (Ensembl)
SMCR8ProteinQ8TEV9 (Uniprot-TrEMBL)
SREB2ProteinP60893 (Uniprot-TrEMBL)
SREBF1GeneProductENSG00000072310 (Ensembl)
STAT3ProteinP40763 (Uniprot-TrEMBL)
TCTE1ProteinQ5JU00 (Uniprot-TrEMBL)
TFE3ProteinP19532 (Uniprot-TrEMBL)
TFEBProteinP19484 (Uniprot-TrEMBL)
TLR4ProteinO00206 (Uniprot-TrEMBL)
TNF-α signaling pathway PathwayWP231 (WikiPathways)
TNFProteinP01375 (Uniprot-TrEMBL)
TNFRSF13BGeneProductENSG00000240505 (Ensembl)
  • CD267, CVID, CVID2, RYZN, TACI, TNFRSF14B are synonyms
  • expressed on CD27+ B memory cells
  • receptor for TNFSF 13 and BAFF
TNFSF13ProteinO75888 (Uniprot-TrEMBL) APRIL is a synonym of TNFSF13
TOLLIPProteinQ9H0E2 (Uniprot-TrEMBL)
TOM1L2GeneProductENSG00000175662 (Ensembl)
TOM1L2ProteinQ6ZVM7 (Uniprot-TrEMBL)
TOP3AGeneProductENSG00000177302 (Ensembl)
TOP3AProteinQ13472 (Uniprot-TrEMBL)
TP53ProteinP04637 (Uniprot-TrEMBL)
TRAF3IP1ProteinQ8TDR0 (Uniprot-TrEMBL)
TTC26ProteinA0AVF1 (Uniprot-TrEMBL)
TTC30BProteinQ8N4P2 (Uniprot-TrEMBL)
Thymine Metabolite17821 (ChEBI)
UBP8ProteinP40818 (Uniprot-TrEMBL)
ULK1 complexComplexCPX-373 (Complex Portal)
ULK1ProteinO75385 (Uniprot-TrEMBL)
UracilMetabolite17568 (ChEBI)
WDR26ProteinQ9H7D7 (Uniprot-TrEMBL)
WDR41ProteinQ9HAD4 (Uniprot-TrEMBL)
WWTR1ProteinQ9GZV5 (Uniprot-TrEMBL)
Y RNAGeneProductENSG00000201378 (Ensembl) misc RNA
YAP1ProteinP46937 (Uniprot-TrEMBL)
Zinc 2+ Metabolite29105 (ChEBI)
cardiolipinMetabolite28494 (ChEBI)
cell cyclePathwayWP179 (WikiPathways)
cortisolMetabolite17650 (ChEBI)
diacylglycerolMetabolite85694 (ChEBI)
glycineMetabolite57305 (ChEBI)
glycolysisPathwayWP534 (WikiPathways)
lipin familyProteinIPR026058 (InterPro)
mRNA Metabolite33699 (ChEBI) demethylation of N6-methyladenosine (m6A)
melatoninMetabolite16796 (ChEBI)
noncanonical NF-kB pathwayPathwayR-HSA-5676590 (Reactome)
one-carbon compoundMetabolite64708 (ChEBI)
phosphatidate Metabolite57739 (ChEBI)
phosphatidylcholineMetabolite64482 (ChEBI)
pyridoxal 5'-phosphate(2-)Metabolite597326 (ChEBI) cofactor
synaptogenesis and neurogenesisPathwayWP5231 (WikiPathways)

Annotated Interactions

No annotated interactions

Retrieved from "https://classic.wikipathways.org/index.php/Pathway:WP5381"
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