15q25 copy number variation (WP5408)

Homo sapiens

15q25.2 or generally 15q25 copy number variations are rare genetic disorders that cause neuropsychiatric disorders, developmental delay and cardiac abnormalities. The exact chromosomal position for this pathway (chr15:83219735-85722039, GRCh37) was taken from Kirov et al. 2014 10.1016/j.biopsych.2013.07.022 and literature cited there.

Authors

Friederike Ehrhart , Alex Pico , Pierre Klemmer , Eric Weitz , and Egon Willighagen

Activity

last edited

Discuss this pathway

Check for ongoing discussions or start your own.

Cited In

Are you planning to include this pathway in your next publication? See How to Cite and add a link here to your paper once it's online.

Organisms

Homo sapiens

Communities

Annotations

Disease Ontology

chromosome 15q25 deletion syndrome

Pathway Ontology

disease pathway

Participants

Label Type Compact URI Comment
Adenosine Metabolite chebi:16335
Thymidine Metabolite chebi:17748
L-threonine residue Metabolite chebi:30013
O-phospho-L-serine residue Metabolite chebi:83421
Cytidine Metabolite chebi:17562
Uridine Metabolite chebi:16704
ADP Metabolite chebi:456216
cAMP Metabolite chebi:58165
AMP Metabolite chebi:456215
ATP Metabolite chebi:30616
O-phospho-L-threonine residue Metabolite chebi:61977
L-serine residue Metabolite chebi:29999
MIR4515 GeneProduct ensembl:ENSG00000263643
AP3B2 GeneProduct uniprot:Q13367
AP3D1 GeneProduct uniprot:O14617
AP3M2 GeneProduct uniprot:P53677
AP3S1 GeneProduct uniprot:Q92572
GRM1 GeneProduct ensembl:ENSG00000152822
RYR2 GeneProduct ensembl:ENSG00000198626
DNM3 GeneProduct ensembl:ENSG00000197959
PDE8A GeneProduct ensembl:ENSG00000073417
RAMAC GeneProduct ensembl:ENSG00000169612 FAM103A1
GOLGA6L4 GeneProduct ensembl:ENSG00000184206
SH3GL3 GeneProduct ensembl:ENSG00000140600
ADAMTSL3 GeneProduct ensembl:ENSG00000156218
RAF1 GeneProduct ensembl:ENSG00000132155
C15orf40 GeneProduct ensembl:ENSG00000169609
NMB GeneProduct ensembl:ENSG00000197696
EGF GeneProduct ensembl:ENSG00000138798
HOMER2 GeneProduct ensembl:ENSG00000103942
SEC11A GeneProduct ensembl:ENSG00000140612
FSD2 GeneProduct ensembl:ENSG00000186628
RYR1 GeneProduct ensembl:ENSG00000196218
WDR73 GeneProduct ensembl:ENSG00000177082
BTBD1 GeneProduct ensembl:ENSG00000064726
SHANK1 GeneProduct ensembl:ENSG00000161681
SYNJ1 GeneProduct ensembl:ENSG00000159082
SPCS3 GeneProduct ensembl:ENSG00000129128
SLC2A1 GeneProduct ensembl:ENSG00000117394 GLUT1
WHAMM GeneProduct ensembl:ENSG00000156232
BNC1 GeneProduct ensembl:ENSG00000169594
CPEB1 GeneProduct ensembl:ENSG00000214575
AP3B2 GeneProduct ensembl:ENSG00000103723
SPCS1 GeneProduct ensembl:ENSG00000114902
NMBR GeneProduct ensembl:ENSG00000135577
AGAP2 GeneProduct ensembl:ENSG00000135439
TOP1 GeneProduct ensembl:ENSG00000198900
ALPK3 GeneProduct ensembl:ENSG00000136383
ITPR1 GeneProduct ensembl:ENSG00000150995
RNMT GeneProduct ensembl:ENSG00000101654
GRM5 GeneProduct ensembl:ENSG00000168959
UBE2Q2L GeneProduct ensembl:ENSG00000259511
SLC28A1 GeneProduct ensembl:ENSG00000156222
HTT GeneProduct ensembl:ENSG00000197386
SPCS2 GeneProduct ensembl:ENSG00000118363
TM6SF1 GeneProduct ensembl:ENSG00000136404
SHANK3 GeneProduct ensembl:ENSG00000251322
ZSCAN2 GeneProduct ensembl:ENSG00000176371
ZNF592 GeneProduct ensembl:ENSG00000166716
TENT4B GeneProduct ensembl:ENSG00000121274 GLD4

References

  1. Association of basonuclin with ability of keratinocytes to multiply and with absence of terminal differentiation. Tseng H, Green H. J Cell Biol. 1994 Jul;126(2):495–506. PubMed Europe PMC Scholia
  2. Homer binds a novel proline-rich motif and links group 1 metabotropic glutamate receptors with IP3 receptors. Tu JC, Xiao B, Yuan JP, Lanahan AA, Leoffert K, Li M, et al. Neuron. 1998 Oct;21(4):717–26. PubMed Europe PMC Scholia
  3. SH3GL3 associates with the Huntingtin exon 1 protein and promotes the formation of polygln-containing protein aggregates. Sittler A, Wälter S, Wedemeyer N, Hasenbank R, Scherzinger E, Eickhoff H, et al. Mol Cell. 1998 Oct;2(4):427–36. PubMed Europe PMC Scholia
  4. The SH3 domains of endophilin and amphiphysin bind to the proline-rich region of synaptojanin 1 at distinct sites that display an unconventional binding specificity. Cestra G, Castagnoli L, Dente L, Minenkova O, Petrelli A, Migone N, et al. J Biol Chem. 1999 Nov 5;274(45):32001–7. PubMed Europe PMC Scholia
  5. Neuromedin B. Ohki-Hamazaki H. Prog Neurobiol. 2000 Oct;62(3):297–312. PubMed Europe PMC Scholia
  6. Characterization of BTBD1 and BTBD2, two similar BTB-domain-containing Kelch-like proteins that interact with Topoisomerase I. Xu L, Yang L, Hashimoto K, Anderson M, Kohlhagen G, Pommier Y, et al. BMC Genomics. 2002;3:1. PubMed Europe PMC Scholia
  7. Homer regulates gain of ryanodine receptor type 1 channel complex. Feng W, Tu J, Yang T, Vernon PS, Allen PD, Worley PF, et al. J Biol Chem. 2002 Nov 22;277(47):44722–30. PubMed Europe PMC Scholia
  8. WHAMM is an Arp2/3 complex activator that binds microtubules and functions in ER to Golgi transport. Campellone KG, Webb NJ, Znameroski EA, Welch MD. Cell. 2008 Jul 11;134(1):148–61. PubMed Europe PMC Scholia
  9. Kinetic and structural studies of phosphodiesterase-8A and implication on the inhibitor selectivity. Wang H, Yan Z, Yang S, Cai J, Robinson H, Ke H. Biochemistry. 2008 Dec 2;47(48):12760–8. PubMed Europe PMC Scholia
  10. CAMOS, a nonprogressive, autosomal recessive, congenital cerebellar ataxia, is caused by a mutant zinc-finger protein, ZNF592. Nicolas E, Poitelon Y, Chouery E, Salem N, Levy N, Mégarbané A, et al. Eur J Hum Genet. 2010 Oct;18(10):1107–13. PubMed Europe PMC Scholia
  11. RAM/Fam103a1 is required for mRNA cap methylation. Gonatopoulos-Pournatzis T, Dunn S, Bounds R, Cowling VH. Mol Cell. 2011 Nov 18;44(4):585–96. PubMed Europe PMC Scholia
  12. Phosphodiesterase-8A binds to and regulates Raf-1 kinase. Brown KM, Day JP, Huston E, Zimmermann B, Hampel K, Christian F, et al. Proc Natl Acad Sci U S A. 2013 Apr 16;110(16):E1533-42. PubMed Europe PMC Scholia
  13. A fly trap mechanism provides sequence-specific RNA recognition by CPEB proteins. Afroz T, Skrisovska L, Belloc E, Guillén-Boixet J, Méndez R, Allain FHT. Genes Dev. 2014 Jul 1;28(13):1498–514. PubMed Europe PMC Scholia
  14. Biallelic Truncating Mutations in ALPK3 Cause Severe Pediatric Cardiomyopathy. Almomani R, Verhagen JMA, Herkert JC, Brosens E, van Spaendonck-Zwarts KY, Asimaki A, et al. J Am Coll Cardiol. 2016 Feb 9;67(5):515–25. PubMed Europe PMC Scholia
  15. ALPK3-deficient cardiomyocytes generated from patient-derived induced pluripotent stem cells and mutant human embryonic stem cells display abnormal calcium handling and establish that ALPK3 deficiency underlies familial cardiomyopathy. Phelan DG, Anderson DJ, Howden SE, Wong RCB, Hickey PF, Pope K, et al. Eur Heart J. 2016 Sep 1;37(33):2586–90. PubMed Europe PMC Scholia
  16. Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM. Varshney D, Petit AP, Bueren-Calabuig JA, Jansen C, Fletcher DA, Peggie M, et al. Nucleic Acids Res. 2016 Dec 1;44(21):10423–36. PubMed Europe PMC Scholia
  17. Essential role for non-canonical poly(A) polymerase GLD4 in cytoplasmic polyadenylation and carbohydrate metabolism. Shin J, Paek KY, Ivshina M, Stackpole EE, Richter JD. Nucleic Acids Res. 2017 Jun 20;45(11):6793–804. PubMed Europe PMC Scholia
  18. ALPK3 gene mutation in a patient with congenital cardiomyopathy and dysmorphic features. Çağlayan AO, Sezer RG, Kaymakçalan H, Ulgen E, Yavuz T, Baranoski JF, et al. Cold Spring Harb Mol Case Stud. 2017 Sep 1;3(5):a001859. PubMed Europe PMC Scholia
  19. Novel ALPK3 mutation in a Tunisian patient with pediatric cardiomyopathy and facio-thoraco-skeletal features. Jaouadi H, Kraoua L, Chaker L, Atkinson A, Delague V, Levy N, et al. J Hum Genet. 2018 Oct;63(10):1077–82. PubMed Europe PMC Scholia
  20. Structure of the human signal peptidase complex reveals the determinants for signal peptide cleavage. Liaci AM, Steigenberger B, Telles de Souza PC, Tamara S, Gröllers-Mulderij M, Ogrissek P, et al. Mol Cell. 2021 Oct 7;81(19):3934-3948.e11. PubMed Europe PMC Scholia