Gene Gene information from NCBI Gene database.
Entrez ID 64131
Gene name Xylosyltransferase 1
Gene symbol XYLT1
Synonyms (NCBI Gene)
DBQD2PXYLT1XT-IXT1XTIXYLTIxylT-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 g
SNPs SNP information provided by dbSNP.
6
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
miRNA miRNA information provided by mirtarbase database.
400
miRTarBase ID miRNA Experiments Reference
MIRT051176 hsa-miR-16-5p CLASH 23622248
MIRT1497738 hsa-let-7a CLIP-seq
MIRT1497739 hsa-let-7b CLIP-seq
MIRT1497740 hsa-let-7c CLIP-seq
MIRT1497741 hsa-let-7d CLIP-seq
Gene ontology (GO) Gene Ontology (GO) annotations describing the biological processes, molecular functions, and cellular components associated with a gene.
28
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 IEA
GO:0000139 Component Golgi membrane TAS
GO:0005576 Component Extracellular region IEA
Other IDs Other IDs provides unique identifiers for this gene in OMIM, HGNC, and Ensembl databases.
MIM HGNC e!Ensembl
608124 15516 ENSG00000103489
Protein Protein information from UniProt database.
UniProt ID Unique identifier for the protein in the UniProt database. Click to view detailed protein information.
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:2
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
Tissue specificity TISSUE SPECIFICITY: Widely expressed. Expressed at higher level in placenta, kidney and pancreas. Weakly expressed in skeletal muscle. {ECO:0000269|PubMed:11099377}.
Sequence
MVAAPCARRLARRSHSALLAALTVLLLQTLVVWNFSSLDSGAGERRGGAAVGGGEQPPPA
PAPRRERRDLPAEPAAARGGGGGGGGGGGGRGPQARARGGGPGEPRGQQPASRGALPARA
LDPHPSPLITLETQDGYFSHRPKEKVRTDSNNENSVPKDFENVDNSNFAPRTQKQKHQPE
LAKKPPSRQKELLKRKLEQQEKGKGHTFPGKGPGEVLPPGDRAAANSSHGKDVSRPPHAR
KTGGSSPETKYDQPPKCDISGKEAISALSRAKSKHCRQEIGETYCRHKLGLLMPEKVTRF
CPLEGKANKNVQWDEDSVEYMPANPVRIAFVLVVHGRASRQLQRMFKAIYHKDHFYYIHV
DKRSNYLHRQVLQVSRQYSNVRVTPWRMATIWGGASLLSTYLQSMRDLLEMTDWPWDFFI
NLSAADYPIRTNDQLVAFLSRYRDMNFLKSHGRDNARFIRKQGLDRLFLECDAHMWRLGD
RRIPEGIAVDGGSDWFLLNRRFVEYVTFSTDDLVTKMKQFYSYTLLPAESFFHTVLENSP
HCDTMVDNNLRITNWNRKLGCKCQYKHIVDWCGCSPNDFKPQD
FHRFQQTARPTFFARKF
EAVVNQEIIGQLDYYLYGNYPAGTPGLRSYWENVYDEPDGIHSLSDVTLTLYHSFARLGL
RRAETSLHTDGENSCRYYPMGHPASVHLYFLADRFQGFLIKHHATNLAVSKLETLETWVM
PKKVFKIASPPSDFGRLQFSEVGTDWDAKERLFRNFGGLLGPMDEPVGMQKWGKGPNVTV
TVIWVDPVNVIAA
TYDILIESTAEFTHYKPPLNLPLRPGVWTVKILHHWVPVAETKFLVA
PLTFSNRQPIKPEEALKLHNGPLRNAYMEQSFQSLNPVLSLPINPAQVEQARRNAASTGT
ALEGWLDSLVGGMWTAMDICATGPTACPVMQTCSQTAWSSFSPDPKSELGAVKPDGRLR
Sequence length 959
Interactions View interactions
Associated diseases Disease associations from ClinVar (causal & non-causal) and other databases (OMIM, Orphanet, GWAS, etc.).
44
Evidence Score: ★☆☆☆☆  Gene-disease association found in Text Mining only ★★☆☆☆  Found in Text Mining and Unknown/Other Associations ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Phenotype Name Clinical Significance dbSNP ID RCV Accession Evidence Score
Desbuquois dysplasia 1 Pathogenic; Likely pathogenic rs587777368, rs1320125389, rs2506152416, rs2507321527, rs2506186149, rs1323802111, rs1164720535 RCV003495110
RCV003064329
RCV002741580
RCV003494646
RCV003598386
View all (2 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Desbuquois dysplasia 2 Pathogenic; Likely pathogenic rs776422861, rs587777366, rs587777368, rs587777369, rs587777370, rs2033685902, rs1085307563, rs1567215600, rs1567215615, rs1567300982 RCV003225190
RCV000115033
RCV000115035
RCV000115036
RCV000115038
View all (5 more)
★★★★★
ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Phenotype Name Clinical Significance Source Evidence Score
Adrenocortical carcinoma, hereditary Likely benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ALZHEIMER DISEASE GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
ATTENTION DEFICIT HYPERACTIVITY DISORDER GWAS catalog
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Autosomal recessive inherited pseudoxanthoma elasticum Uncertain significance; Likely benign; Benign ClinVar
★★☆☆☆
Found in Text Mining + Unknown/Other Associations
Associations from Text Mining Disease associations identified through text mining
Disease Name Disease (Merged) Source PMID Relationship Type Evidence Score
Acne Acne HPO_DG
★☆☆☆☆
Found in Text Mining only
Age related macular degeneration Age-related macular degeneration HPO_DG
★☆☆☆☆
Found in Text Mining only
Angioid Streaks Angioid streaks HPO_DG
★☆☆☆☆
Found in Text Mining only
Aortic Aneurysm, Abdominal Aortic Aneurysm BEFREE 18294457
★☆☆☆☆
Found in Text Mining only
Aortic Aneurysm, Abdominal Aortic Aneurysm LHGDN 18294457
★☆☆☆☆
Found in Text Mining only
Arnold-Chiari Malformation, Type I Arnold-Chiari malformation BEFREE 25609184
★☆☆☆☆
Found in Text Mining only
Astrocytoma Astrocytoma BEFREE 29157673
★☆☆☆☆
Found in Text Mining only
Barber Say syndrome Barber Say Syndrome BEFREE 30554721
★☆☆☆☆
Found in Text Mining only
Bernard-Soulier Syndrome Bernard Soulier Syndrome BEFREE 30554721
★☆☆☆☆
Found in Text Mining only
Blood Coagulation Disorders Blood coagulation disorder Pubtator 35005846 Associate
★☆☆☆☆
Found in Text Mining only