XYLT2 xylosyltransferase 2 [Homo sapiens (human)] - Gene

Summary

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: mouse all
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Genomic context

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_000017.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

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Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
HEK293 cells lacking both XT-isoforms are not viable
Title: Xylosyltransferase-deficient human HEK293 cells show a strongly reduced proliferation capacity and viability.
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.
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.
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.
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.
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.
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.
Seven XYLT2 promoter single nucleotide variants (SNVs) were identified and genotyped.
Title: Identification and characterization of human xylosyltransferase II promoter single nucleotide variants.

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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	Compare labs
Spondylo-ocular syndrome MedGen: C4225412 OMIM: 605822 GeneReviews: Not available	Compare labs

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D8S2279 (e-PCR)
- UniSTS:473907

D1S1423 (e-PCR)
- UniSTS:149619

D16S325 (e-PCR)
- UniSTS:147089

RH69808 (e-PCR)
- UniSTS:56270

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

EC 2.4.2.26

XP_005257629.1

EC 2.4.2.26

XP_047292478.1

EC 2.4.2.26

XP_054172872.1

EC 2.4.2.26

XP_054172873.1

EC 2.4.2.26

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

NG_012175.1 RefSeqGene

Range

5095..20154

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

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

NC_000017.11 Reference GRCh38.p14 Primary Assembly

Range

50346126..50361185

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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
XM_047436522.1 → XP_047292478.1 xylosyltransferase 2 isoform X2