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XYLT2 xylosyltransferase 2 [ Homo sapiens (human) ]

Gene ID: 64132, updated on 5-Mar-2024

Summary

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Official Symbol
XYLT2provided by HGNC
Official Full Name
xylosyltransferase 2provided by HGNC
Primary source
HGNC:HGNC:15517
See related
Ensembl:ENSG00000015532 MIM:608125; AllianceGenome:HGNC:15517
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SOS; XT2; XT-II; PXYLT2; xylT-II
Summary
The protein encoded by this gene is an isoform of xylosyltransferase, which belongs to a family of glycosyltransferases. This enzyme transfers xylose from UDP-xylose to specific serine residues of the core protein and initiates the biosynthesis of glycosaminoglycan chains in proteoglycans including chondroitin sulfate, heparan sulfate, heparin and dermatan sulfate. The enzyme activity, which is increased in scleroderma patients, is a diagnostic marker for the determination of sclerotic activity in systemic sclerosis. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Dec 2013]
Expression
Ubiquitous expression in stomach (RPKM 12.9), testis (RPKM 8.6) and 25 other tissues See more
Orthologs
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Genomic context

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See XYLT2 in Genome Data Viewer
Location:
17q21.33
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (50346126..50361185)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (51213470..51228147)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (48423487..48438546)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8692 Neighboring gene Sharpr-MPRA regulatory region 4171 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48354331-48354878 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:48354879-48355426 Neighboring gene transmembrane protein 92 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8693 Neighboring gene TMEM92 antisense RNA 1 Neighboring gene NANOG hESC enhancer GRCh37_chr17:48380397-48381379 Neighboring gene NANOG hESC enhancer GRCh37_chr17:48388769-48389287 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12381 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr17:48395384-48395963 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:48395964-48396542 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8694 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8695 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8696 Neighboring gene Sharpr-MPRA regulatory region 10047 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:48448134-48448295 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12382 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12383 Neighboring gene mitochondrial ribosomal protein L27 Neighboring gene essential meiotic structure-specific endonuclease 1 Neighboring gene leucine rich repeat containing 59

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Intrafamilial variability of XYLT2-related spondyloocular syndrome. Guleray N, et al. Eur J Med Genet, 2019 Nov. PMID 30496831
  2. Homozygous XYLT2 variants as a cause of spondyloocular syndrome. Umair M, et al. Clin Genet, 2018 Apr. PMID 29136277
  3. Abnormal Proteoglycan Synthesis Due to Gene Defects Causes Skeletal Diseases with Overlapping Phenotypes. Taylan F, et al. Horm Metab Res, 2016 Nov. PMID 27871115
  4. Spondyloocular Syndrome: Novel Mutations in XYLT2 Gene and Expansion of the Phenotypic Spectrum. Taylan F, et al. J Bone Miner Res, 2016 Aug. PMID 26987875
  5. Identification and characterization of human xylosyltransferase II promoter single nucleotide variants. Faust I, et al. Biochem Biophys Res Commun, 2015 Mar 20. PMID 25704086

See all (43) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Development of a xylosyltransferase-I-selective UPLC MS/MS activity assay using a specific acceptor peptide.
    Title: Development of a xylosyltransferase-I-selective UPLC MS/MS activity assay using a specific acceptor peptide.
  2. Expression of xylosyltransferases I and II and their role in the pathogenesis of arthrofibrosis.
    Title: Expression of xylosyltransferases I and II and their role in the pathogenesis of arthrofibrosis.
  3. HEK293 cells lacking both XT-isoforms are not viable
    Title: Xylosyltransferase-deficient human HEK293 cells show a strongly reduced proliferation capacity and viability.
  4. We report on two siblings with spondyloocular syndrome who presented with varying clinical severity. A novel XYLT2 missense mutation was detected in a region evolutionary conserved across the species
    Title: Intrafamilial variability of XYLT2-related spondyloocular syndrome.
  5. Using DNA from affected members of the same 2 families, we performed whole exome sequencing, which revealed 2 novel homozygous missense variants (c.1159C > T, p.Arg387Trp) and (c.2548G > C, p.Asp850His). Our findings extend the body of evidence that SOS is caused by homozygous variants in the XYLT2 gene
    Title: Homozygous XYLT2 variants as a cause of spondyloocular syndrome.
  6. mutations in the XYLT2 gene result in a variable phenotype dominated by spinal osteoporosis, cataract, and hearing loss.
    Title: Spondyloocular Syndrome: Novel Mutations in XYLT2 Gene and Expansion of the Phenotypic Spectrum.
  7. XYLT2 mutations cause a relatively distinct phenotype, the so-called spondyloocular syndrome.
    Title: Abnormal Proteoglycan Synthesis Due to Gene Defects Causes Skeletal Diseases with Overlapping Phenotypes.
  8. Homozygosity for frameshift mutations in XYLT2 result in a spondylo-ocular syndrome with bone fragility, cataracts, and hearing defects.
    Title: Homozygosity for frameshift mutations in XYLT2 result in a spondylo-ocular syndrome with bone fragility, cataracts, and hearing defects.
  9. Demonstrate that XT-II is the predominant isoenzyme responsible for XT activity in serum. The proof was performed using UDP-xylose as the xylose donor, as well as the compound UDP-4-azido-4-deoxyxylose, which is a selective xylose donor for XT-I.
    Title: Xylosyltransferase II is the predominant isoenzyme which is responsible for the steady-state level of xylosyltransferase activity in human serum.
  10. Seven XYLT2 promoter single nucleotide variants (SNVs) were identified and genotyped.
    Title: Identification and characterization of human xylosyltransferase II promoter single nucleotide variants.
Submit: New GeneRIF Correction See all GeneRIFs (21)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Autosomal recessive inherited pseudoxanthoma elasticum
MedGen: C1275116 OMIM: 264800 GeneReviews: Pseudoxanthoma Elasticum
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Spondylo-ocular syndrome
MedGen: C4225412 OMIM: 605822 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables magnesium ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables manganese ion binding IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein xylosyltransferase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein xylosyltransferase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein xylosyltransferase activity NAS
Non-traceable Author Statement
more info
 PubMed 
enables protein xylosyltransferase activity TAS
Traceable Author Statement
more info
  
Process Evidence Code Pubs
involved_in chondroitin sulfate biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in chondroitin sulfate proteoglycan biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in chondroitin sulfate proteoglycan biosynthetic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in glycosaminoglycan biosynthetic process NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in glycosaminoglycan metabolic process TAS
Traceable Author Statement
more info
  
involved_in heparan sulfate proteoglycan biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in heparan sulfate proteoglycan biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
involved_in heparan sulfate proteoglycan biosynthetic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in heparin biosynthetic process IEA
Inferred from Electronic Annotation
more info
  
Component Evidence Code Pubs
located_in Golgi membrane TAS
Traceable Author Statement
more info
  
located_in extracellular space IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
xylosyltransferase 2
Names
UDP-D-xylose:proteoglycan core protein beta-D-xylosyltransferase
peptide O-xylosyltransferase 1
protein xylosyltransferase 2
xylosyltransferase II
NP_071450.2
XP_005257629.1
XP_047292478.1
XP_054172872.1
XP_054172873.1

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_012175.1 RefSeqGene

    Range
    5095..20154
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_022167.4 → NP_071450.2  xylosyltransferase 2

    See identical proteins and their annotated locations for NP_071450.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the protein-coding transcript.
    Source sequence(s)
    AJ277442, AK299999, BM726479, BQ018370
    Consensus CDS
    CCDS11563.1
    UniProtKB/Swiss-Prot
    Q6UY41, Q86V00, Q9H1B5
    Related
    ENSP00000017003.2, ENST00000017003.7
    Conserved Domains (2) summary
    pfam02485
    Location:234 → 486
    Branch; Core-2/I-Branching enzyme
    pfam12529
    Location:519 → 699
    Xylo_C; Xylosyltransferase C terminal

RNA

  1. NR_110010.2 RNA Sequence

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 3' region compared to variant 1. It is represented as non-coding because the use of the 5'-most translational start codon, as used in variant 1, renders this transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AJ277442, AY358090, BM726479, BQ018370
    Related
    ENST00000376550.7

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    50346126..50361185
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005257572.5 → XP_005257629.1  xylosyltransferase 2 isoform X1

    Conserved Domains (2) summary
    pfam02485
    Location:202 → 454
    Branch; Core-2/I-Branching enzyme
    pfam12529
    Location:487 → 667
    Xylo_C; Xylosyltransferase C terminal

  2. XM_047436522.1 → XP_047292478.1  xylosyltransferase 2 isoform X2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    51213470..51228147
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054316897.1 → XP_054172872.1  xylosyltransferase 2 isoform X1

  2. XM_054316898.1 → XP_054172873.1  xylosyltransferase 2 isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H1B5.2 GenPept UniProtKB/Swiss-Prot:Q9H1B5

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