X-linked intellectual disability

Several X-linked syndromes include intellectual disability as part of the presentation. These include:

• Coffin–Lowry syndrome
• DDX3X syndrome
• MASA syndrome
• MECP2 duplication syndrome
• Mental retardation and microcephaly with pontine and cerebellar hypoplasia
• X-linked alpha thalassemia mental retardation syndrome

Following is a list of genes located on the X chromosome and linked to intellectual disability. There are also several loci that have not been associated with a specific gene.

• IQSEC2: encodes an exchange factor for the Arf family of small GTP binding proteins, involved in the formation of secretory vesicles.{{cite journal | vauthors = Shoubridge C, Tarpey PS, Abidi F, Ramsden SL, Rujirabanjerd S, Murphy JA, Boyle J, Shaw M, Gardner A, Proos A, Puusepp H, Raymond FL, Schwartz CE, Stevenson RE, Turner G, Field M, Walikonis RS, Harvey RJ, Hackett A, Futreal PA, Stratton MR, Gécz J | display-authors = 6 | title = Mutations in the guanine nucleotide exchange factor gene IQSEC2 cause nonsyndromic intellectual disability | journal = Nature Genetics | volume = 42 | issue = 6 | pages = 486–488 | date = June 2010 | pmid = 20473311 | pmc = 3632837 | doi = 10.1038/ng.588 }}
• TM4SF2: is a member of the 4 transmembrane domains family of proteins (tetraspanins, see TSPAN7). This gene is also associated with neuropsychiatric diseases such as Huntington's chorea.{{cite journal | vauthors = Abidi FE, Holinski-Feder E, Rittinger O, Kooy F, Lubs HA, Stevenson RE, Schwartz CE | title = A novel 2 bp deletion in the TM4SF2 gene is associated with MRX58 | journal = Journal of Medical Genetics | volume = 39 | issue = 6 | pages = 430–433 | date = June 2002 | pmid = 12070254 | pmc = 1735161 | doi = 10.1136/jmg.39.6.430 }}
• AP1S2: AP-1 complex subunit sigma-2.{{cite journal | vauthors = Tarpey PS, Stevens C, Teague J, Edkins S, O'Meara S, Avis T, Barthorpe S, Buck G, Butler A, Cole J, Dicks E, Gray K, Halliday K, Harrison R, Hills K, Hinton J, Jones D, Menzies A, Mironenko T, Perry J, Raine K, Richardson D, Shepherd R, Small A, Tofts C, Varian J, West S, Widaa S, Yates A, Catford R, Butler J, Mallya U, Moon J, Luo Y, Dorkins H, Thompson D, Easton DF, Wooster R, Bobrow M, Carpenter N, Simensen RJ, Schwartz CE, Stevenson RE, Turner G, Partington M, Gecz J, Stratton MR, Futreal PA, Raymond FL | display-authors = 6 | title = Mutations in the gene encoding the Sigma 2 subunit of the adaptor protein 1 complex, AP1S2, cause X-linked mental retardation | journal = American Journal of Human Genetics | volume = 79 | issue = 6 | pages = 1119–1124 | date = December 2006 | pmid = 17186471 | pmc = 1698718 | doi = 10.1086/510137 }}{{cite web | work = Entrez Gene | title = AP1S2 adaptor-related protein complex 1, sigma 2 subunit | publisher = National Center for Biotechnology Information, U.S. National Library of Medicine |url=https://www.ncbi.nlm.nih.gov/sites/entrez?Db=gene&Cmd=ShowDetailView&TermToSearch=8905 }} Adaptor protein complex 1 is found on the cytoplasmic face of vesicles located at the Golgi complex, where it mediates both the recruitment of clathrin to the membrane and the recognition of sorting signals within the cytosolic tails of transmembrane receptors.
• ACSL4: Long-chain-fatty-acid—CoA ligase 4 is an enzyme of the long-chain fatty-acid-coenzyme A ligase family. It converts free long-chain fatty acids into fatty acyl-CoA esters, and thereby play a key role in lipid biosynthesis and fatty acid degradation.{{cite journal | vauthors = Piccini M, Vitelli F, Bruttini M, Pober BR, Jonsson JJ, Villanova M, Zollo M, Borsani G, Ballabio A, Renieri A | display-authors = 6 | title = FACL4, a new gene encoding long-chain acyl-CoA synthetase 4, is deleted in a family with Alport syndrome, elliptocytosis, and mental retardation | journal = Genomics | volume = 47 | issue = 3 | pages = 350–358 | date = February 1998 | pmid = 9480748 | doi = 10.1006/geno.1997.5104 | doi-access = free }} This isozyme preferentially utilizes arachidonate as substrate.
• ZNF41: Zinc finger protein 41 is a likely zinc finger family transcription factor.{{cite journal | vauthors = Franzè A, Archidiacono N, Rocchi M, Marino M, Grimaldi G | title = Isolation and expression analysis of a human zinc finger gene (ZNF41) located on the short arm of the X chromosome | journal = Genomics | volume = 9 | issue = 4 | pages = 728–736 | date = April 1991 | pmid = 2037297 | doi = 10.1016/0888-7543(91)90367-N }}
• DLG3: Disks large homolog 3, also named neuroendocrine-DLG or synapse-associated protein 102 (SAP-102).{{cite journal | vauthors = Stathakis DG, Lee D, Bryant PJ | title = DLG3, the gene encoding human neuroendocrine Dlg (NE-Dlg), is located within the 1.8-Mb dystonia-parkinsonism region at Xq13.1 | journal = Genomics | volume = 49 | issue = 2 | pages = 310–313 | date = April 1998 | pmid = 9598320 | doi = 10.1006/geno.1998.5243 }} DLG3 is a member of the membrane-associated guanylate kinase (MAGUK) superfamily.
• FTSJ1: Transfert RNA methyltransferase 1 is a member of the S-adenosylmethionine-binding protein family. This nucleolar protein is involved in the processing and modification of tRNA.{{cite journal | vauthors = Ramser J, Winnepenninckx B, Lenski C, Errijgers V, Platzer M, Schwartz CE, Meindl A, Kooy RF | display-authors = 6 | title = A splice site mutation in the methyltransferase gene FTSJ1 in Xp11.23 is associated with non-syndromic mental retardation in a large Belgian family (MRX9) | journal = Journal of Medical Genetics | volume = 41 | issue = 9 | pages = 679–683 | date = September 2004 | pmid = 15342698 | pmc = 1735884 | doi = 10.1136/jmg.2004.019000 }}{{cite journal | vauthors = Guy MP, Phizicky EM | title = Conservation of an intricate circuit for crucial modifications of the tRNAPhe anticodon loop in eukaryotes | journal = RNA | volume = 21 | issue = 1 | pages = 61–74 | date = January 2015 | pmid = 25404562 | pmc = 4274638 | doi = 10.1261/rna.047639.114 | name-list-style = amp }}
• GDI1: RabGDI alpha makes a complex with geranylgeranylated small GTP-binding proteins of the Rab family and keeps them in the cytosol.
• MECP2: methyl CpG binding protein 2 is a transcription regulator, which represses transcription from methylated gene promoters. It appears to be essential for the normal function of nerve cells.{{cite journal | vauthors = Chahrour M, Jung SY, Shaw C, Zhou X, Wong ST, Qin J, Zoghbi HY | title = MeCP2, a key contributor to neurological disease, activates and represses transcription | journal = Science | volume = 320 | issue = 5880 | pages = 1224–1229 | date = May 2008 | pmid = 18511691 | pmc = 2443785 | doi = 10.1126/science.1153252 | bibcode = 2008Sci...320.1224C }} In contrast to other MBD family members, MECP2 is X-linked and subject to X inactivation. MECP2 gene mutations are the cause of most cases of Rett syndrome, a progressive neurologic developmental disorder and one of the most common causes of intellectual disability in women.
• ARX: Aristaless related homeobox, is a protein associated with intellectual disability and lissencephaly. This gene is a homeobox-containing gene expressed during development. The expressed protein contains two conserved domains, a C-peptide (or aristaless domain) and the prd-like class homeobox domain. It is a member of the group-II aristaless-related protein family whose members are expressed primarily in the central and/or peripheral nervous system. This gene is involved in CNS and pancreas development. Mutations in this gene cause X-linked intellectual disability and epilepsy.{{cite journal | vauthors = Bienvenu T, Poirier K, Friocourt G, Bahi N, Beaumont D, Fauchereau F, Ben Jeema L, Zemni R, Vinet MC, Francis F, Couvert P, Gomot M, Moraine C, van Bokhoven H, Kalscheuer V, Frints S, Gecz J, Ohzaki K, Chaabouni H, Fryns JP, Desportes V, Beldjord C, Chelly J | display-authors = 6 | title = ARX, a novel Prd-class-homeobox gene highly expressed in the telencephalon, is mutated in X-linked mental retardation | journal = Human Molecular Genetics | volume = 11 | issue = 8 | pages = 981–991 | date = April 2002 | pmid = 11971879 | doi = 10.1093/hmg/11.8.981 | doi-access = free }}
• KDM5C: Lysine-specific demethylase 5C is an enzyme that in humans is encoded by the KDM5C gene a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one JmjN domain and two PHD-type zinc fingers. The DNA-binding motifs suggest this protein is involved in the regulation of transcription and chromatin remodeling.{{cite journal | vauthors = Jensen LR, Amende M, Gurok U, Moser B, Gimmel V, Tzschach A, Janecke AR, Tariverdian G, Chelly J, Fryns JP, Van Esch H, Kleefstra T, Hamel B, Moraine C, Gecz J, Turner G, Reinhardt R, Kalscheuer VM, Ropers HH, Lenzner S | display-authors = 6 | title = Mutations in the JARID1C gene, which is involved in transcriptional regulation and chromatin remodeling, cause X-linked mental retardation | journal = American Journal of Human Genetics | volume = 76 | issue = 2 | pages = 227–236 | date = February 2005 | pmid = 15586325 | pmc = 1196368 | doi = 10.1086/427563 }}
• PHF8: PHD finger protein 8 belongs to the family of ferrous iron and 2-oxoglutarate dependent oxygenases,{{cite journal | vauthors = Loenarz C, Schofield CJ | title = Expanding chemical biology of 2-oxoglutarate oxygenases | journal = Nature Chemical Biology | volume = 4 | issue = 3 | pages = 152–156 | date = March 2008 | pmid = 18277970 | doi = 10.1038/nchembio0308-152 | author-link2 = Christopher J. Schofield }} and is a histone lysine demethylase with selectivity for the di-and monomethyl states.{{cite journal | vauthors = Loenarz C, Ge W, Coleman ML, Rose NR, Cooper CD, Klose RJ, Ratcliffe PJ, Schofield CJ | display-authors = 6 | title = PHF8, a gene associated with cleft lip/palate and mental retardation, encodes for an Nepsilon-dimethyl lysine demethylase | journal = Human Molecular Genetics | volume = 19 | issue = 2 | pages = 217–222 | date = January 2010 | pmid = 19843542 | pmc = 4673897 | doi = 10.1093/hmg/ddp480 | author-link8 = Christopher J. Schofield }}
• FMR2: Fragile mental retardation 2 (FMR2: synonym AFF2),{{cite journal | vauthors = Stettner GM, Shoukier M, Höger C, Brockmann K, Auber B | title = Familial intellectual disability and autistic behavior caused by a small FMR2 gene deletion | journal = American Journal of Medical Genetics. Part A | volume = 155A | issue = 8 | pages = 2003–2007 | date = August 2011 | pmid = 21739600 | doi = 10.1002/ajmg.a.34122 | s2cid = 9568277 }} the protein belongs to the AFF family which currently has four members: AFF1/AF4, AFF2/FMR2, AFF3/LAF4 and AFF4/AF5q31.{{cite journal | vauthors = Melko M, Douguet D, Bensaid M, Zongaro S, Verheggen C, Gecz J, Bardoni B | title = Functional characterization of the AFF (AF4/FMR2) family of RNA-binding proteins: insights into the molecular pathology of FRAXE intellectual disability | journal = Human Molecular Genetics | volume = 20 | issue = 10 | pages = 1873–1885 | date = May 2011 | pmid = 21330300 | doi = 10.1093/hmg/ddr069 | doi-access = free }} All AFF proteins are localized in the nucleus and have a role as transcriptional activators with a positive action on RNA elongation. AFF2/FMR2, AFF3/LAF4 and AFF4/AF5q31 localize in nuclear speckles (subnuclear structures considered to be storage/modification sites of pre-mRNA splicing factors) and are able to bind RNA with a high apparent affinity for the G-quadruplex structure. They appear to modulate alternative splicing via the interaction with the G-quadruplex RNA-forming structure.
• Slc6a8: Creatine transporter is a protein that is required for creatine to enter the cell. Creatine is essential for maintaining ATP levels in cells with a high energy demand.{{cite journal | vauthors = Cecil KM, Salomons GS, Ball WS, Wong B, Chuck G, Verhoeven NM, Jakobs C, DeGrauw TJ | display-authors = 6 | title = Irreversible brain creatine deficiency with elevated serum and urine creatine: a creatine transporter defect? | journal = Annals of Neurology | volume = 49 | issue = 3 | pages = 401–404 | date = March 2001 | pmid = 11261517 | doi = 10.1002/ana.79 | s2cid = 38756630 }}
• GSPT2{{cite journal | vauthors = Grau C, Starkovich M, Azamian MS, Xia F, Cheung SW, Evans P, Henderson A, Lalani SR, Scott DA | display-authors = 6 | title = Xp11.22 deletions encompassing CENPVL1, CENPVL2, MAGED1 and GSPT2 as a cause of syndromic X-linked intellectual disability | journal = PLOS ONE | volume = 12 | issue = 4 | pages = e0175962 | year = 2017 | pmid = 28414775 | pmc = 5393878 | doi = 10.1371/journal.pone.0175962 | doi-access = free | bibcode = 2017PLoSO..1275962G }}
• MAGED1{{cite journal | vauthors = Grau C, Starkovich M, Azamian MS, Xia F, Cheung SW, Evans P, Henderson A, Lalani SR, Scott DA | display-authors = 6 | title = Xp11.22 deletions encompassing CENPVL1, CENPVL2, MAGED1 and GSPT2 as a cause of syndromic X-linked intellectual disability | journal = PLOS ONE | volume = 12 | issue = 4 | pages = e0175962 | year = 2017 | pmid = 28414775 | pmc = 5393878 | doi = 10.1371/journal.pone.0175962 | doi-access = free | bibcode = 2017PLoSO..1275962G }}
• UBE2A{{cite journal | vauthors = Czeschik JC, Bauer P, Buiting K, Dufke C, Guillén-Navarro E, Johnson DS, Koehler U, López-González V, Lüdecke HJ, Male A, Morrogh D, Rieß A, Tzschach A, Wieczorek D, Kuechler A | display-authors = 6 | title = X-linked intellectual disability type Nascimento is a clinically distinct, probably underdiagnosed entity | journal = Orphanet Journal of Rare Diseases | volume = 8 | pages = 146 | date = September 2013 | pmid = 24053514 | pmc = 4015352 | doi = 10.1186/1750-1172-8-146 | doi-access = free }}
• OGT{{Cite journal |last=Mayfield |first=Johnathan M. |last2=Hitefield |first2=Naomi L. |last3=Czajewski |first3=Ignacy |last4=Vanhye |first4=Lotte |last5=Holden |first5=Laura |last6=Morava |first6=Eva |last7=van Aalten |first7=Daan M.F. |last8=Wells |first8=Lance |date=September 2024 |title=O-GlcNAc transferase congenital disorder of glycosylation (OGT-CDG): Potential mechanistic targets revealed by evaluating the OGT interactome |url=https://linkinghub.elsevier.com/retrieve/pii/S0021925824021008 |journal=Journal of Biological Chemistry |language=en |volume=300 |issue=9 |pages=107599 |doi=10.1016/j.jbc.2024.107599 |pmc=11381892 |pmid=39059494}}{{Cite journal |last=Cheng |first=Steven S. |last2=Mody |first2=Alison C. |last3=Woo |first3=Christina M. |date=2024-11-07 |title=Opportunities for Therapeutic Modulation of O-GlcNAc |url=https://pubs.acs.org/doi/10.1021/acs.chemrev.4c00417 |journal=Chemical Reviews |language=en |doi=10.1021/acs.chemrev.4c00417 |issn=0009-2665|url-access=subscription }}

• Xp11.2 Duplication

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{{X-linked disorders}}

{{Cell membrane protein disorders}}

{{Deficiencies of intracellular signaling peptides and proteins}}

{{Transcription factor/coregulator deficiencies}}

{{Vesicular transport protein disorders}}

Category:Intellectual disability

Category:X-linked recessive disorders