XYLT1 (xylosyltransferase 1)

Gene

• Entrez ID: 64131
• Gene name: Xylosyltransferase 1
• Gene symbol: XYLT1
• Synonyms: DBQD2, PXYLT1, XT-I, XT1, XTI, XYLTI, xylT-I
• Chromosome: 16
• Chromosome location: 16p12.3
• Summary: This locus encodes a xylosyltransferase enzyme. The encoded protein catalyzes transfer of UDP-xylose to serine residues of an acceptor protein substrate. This transfer reaction is necessary for biosynthesis of glycosaminoglycan chains. Mutations in this gene have been associated with increased severity of pseudoxanthoma elasticum.[provided by RefSeq, Nov 2009]

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs587777366	G>A	Pathogenic	Missense variant, coding sequence variant
rs587777368	G>A,T	Pathogenic	Synonymous variant, stop gained, coding sequence variant
rs587777370	T>G	Pathogenic	Splice acceptor variant
rs769391314	C>A,T	Likely-pathogenic	Genic downstream transcript variant, synonymous variant, stop gained, coding sequence variant, missense variant
rs1323802111	GC>-	Likely-pathogenic	Coding sequence variant, frameshift variant
rs1567300982	C>T	Pathogenic	Splice acceptor variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT051176	hsa-miR-16-5p	CLASH	23622248

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000137	Component	Golgi cis cisterna	ISS
GO:0000139	Component	Golgi membrane	IDA	16571645
GO:0000139	Component	Golgi membrane	TAS
GO:0005615	Component	Extracellular space	IDA	11087729
GO:0006024	Process	Glycosaminoglycan biosynthetic process	TAS	11099377
GO:0015012	Process	Heparan sulfate proteoglycan biosynthetic process	IBA	21873635
GO:0015012	Process	Heparan sulfate proteoglycan biosynthetic process	IEA
GO:0015012	Process	Heparan sulfate proteoglycan biosynthetic process	IMP	17189265
GO:0016021	Component	Integral component of membrane	IEA
GO:0018215	Process	Protein phosphopantetheinylation	IEA
GO:0030158	Function	Protein xylosyltransferase activity	IBA	21873635
GO:0030158	Function	Protein xylosyltransferase activity	IDA	11087729, 17189265, 29681470
GO:0030158	Function	Protein xylosyltransferase activity	TAS	11099377
GO:0030166	Process	Proteoglycan biosynthetic process	IDA	11087729
GO:0030203	Process	Glycosaminoglycan metabolic process	TAS
GO:0030206	Process	Chondroitin sulfate biosynthetic process	IEA
GO:0043931	Process	Ossification involved in bone maturation	ISS
GO:0046872	Function	Metal ion binding	IEA
GO:0048706	Process	Embryonic skeletal system development	ISS
GO:0050650	Process	Chondroitin sulfate proteoglycan biosynthetic process	IBA	21873635
GO:0050650	Process	Chondroitin sulfate proteoglycan biosynthetic process	IMP	17189265

Other IDs

• MIM: 608124
• HGNC: 15516
• e!Ensembl: ENSG00000103489

Protein

• UniProt ID: Q86Y38
• Protein name: Xylosyltransferase 1 (EC 2.4.2.26) (Peptide O-xylosyltransferase 1) (Xylosyltransferase I) (XT-I) (XylT-I)
• Protein function: Catalyzes the first step in the biosynthesis of chondroitin sulfate and dermatan sulfate proteoglycans, such as DCN. Transfers D-xylose from UDP-D-xylose to specific serine residues of the core protein (PubMed:15461586, PubMed:17189265, PubMed:24581741, PubMed:23982343). Required for normal embryonic and postnatal skeleton development, especially of the long bones (PubMed:24581741, PubMed:23982343). Required for normal maturation of chondrocytes during bone development, and normal onset of ossification (By similarity).
• PDB: 6EJ7, 6EJ8, 6EJ9, 6EJA, 6EJB, 6EJC, 6EJD, 6EJE, 6FOA
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF02485	Branch	328 → 583	Core-2/I-Branching enzyme	Family
  PF12529	Xylo_C	613 → 793	Xylosyltransferase C terminal	Family

• Sequence:

  MVAAPCARRLARRSHSALLAALTVLLLQTLVVWNFSSLDSGAGERRGGAAVGGGEQPPPA
  PAPRRERRDLPAEPAAARGGGGGGGGGGGGRGPQARARGGGPGEPRGQQPASRGALPARA
  LDPHPSPLITLETQDGYFSHRPKEKVRTDSNNENSVPKDFENVDNSNFAPRTQKQKHQPE
  LAKKPPSRQKELLKRKLEQQEKGKGHTFPGKGPGEVLPPGDRAAANSSHGKDVSRPPHAR
  KTGGSSPETKYDQPPKCDISGKEAISALSRAKSKHCRQEIGETYCRHKLGLLMPEKVTRF
  CPLEGKANKNVQWDEDSVEYMPANPVRIAFVLVVHGRASRQLQRMFKAIYHKDHFYYIHV
  DKRSNYLHRQVLQVSRQYSNVRVTPWRMATIWGGASLLSTYLQSMRDLLEMTDWPWDFFI
  NLSAADYPIRTNDQLVAFLSRYRDMNFLKSHGRDNARFIRKQGLDRLFLECDAHMWRLGD
  RRIPEGIAVDGGSDWFLLNRRFVEYVTFSTDDLVTKMKQFYSYTLLPAESFFHTVLENSP
  HCDTMVDNNLRITNWNRKLGCKCQYKHIVDWCGCSPNDFKPQDFHRFQQTARPTFFARKF
  EAVVNQEIIGQLDYYLYGNYPAGTPGLRSYWENVYDEPDGIHSLSDVTLTLYHSFARLGL
  RRAETSLHTDGENSCRYYPMGHPASVHLYFLADRFQGFLIKHHATNLAVSKLETLETWVM
  PKKVFKIASPPSDFGRLQFSEVGTDWDAKERLFRNFGGLLGPMDEPVGMQKWGKGPNVTV
  TVIWVDPVNVIAATYDILIESTAEFTHYKPPLNLPLRPGVWTVKILHHWVPVAETKFLVA
  PLTFSNRQPIKPEEALKLHNGPLRNAYMEQSFQSLNPVLSLPINPAQVEQARRNAASTGT
  ALEGWLDSLVGGMWTAMDICATGPTACPVMQTCSQTAWSSFSPDPKSELGAVKPDGRLR

• Sequence length: 959