XYLT1

Chr 16AR

xylosyltransferase 1

Also known as: DBQD2, PXYLT1, XT-I, XT1, XTI, XYLTI, xylT-I

NCBI Gene: 64131ENSG00000103489UniProt: Q86Y38OMIM: 608124

This gene encodes xylosyltransferase 1, which catalyzes the first step in chondroitin sulfate and dermatan sulfate proteoglycan biosynthesis by transferring xylose to serine residues of core proteins. Biallelic mutations cause Desbuquois dysplasia 2, an autosomal recessive skeletal dysplasia, and can modify the severity of pseudoxanthoma elasticum. The gene is highly constrained against loss-of-function variants (pLI 0.92, LOEUF 0.34), reflecting its essential role in skeletal development and proteoglycan synthesis.

GeneReviewsOMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.342 OMIM phenotypes
Clinical Summary— XYLT1
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 0.92). One damaged copy is likely sufficient to cause disease.
📋
ClinVar Variants
51 unique Pathogenic / Likely Pathogenic· 221 VUS of 470 total submissions
Explore recent and relevant literature in Research Assistant →
📖
GeneReview available — XYLT1
Authoritative clinical overview · Recommended first read
Open GeneReview ↗

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.34LOEUF
pLI 0.924
Z-score 4.76
OE 0.18 (0.10–0.34)
Highly constrained

Highly LoF-intolerant (top ~10% of genes)

Missense Constraint
0.59Z-score
OE missense 0.93 (0.86–1.00)
508 obs / 546.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.18 (0.10–0.34)
0≤0.351.4
Missense OE0.93 (0.86–1.00)
0≤0.61.4
Synonymous OE1.14
0≤1.21.6
LoF obs/exp: 7 / 39.1Missense obs/exp: 508 / 546.5Syn Z: -1.62

ClinVar Variant Classifications

470 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic39
Likely Pathogenic12
VUS221
Likely Benign171
Benign10
Conflicting2
39
Pathogenic
12
Likely Pathogenic
221
VUS
171
Likely Benign
10
Benign
2
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
11
2
26
0
39
Likely Pathogenic
3
0
9
0
12
VUS
2
174
45
0
221
Likely Benign
0
5
54
112
171
Benign
0
0
5
5
10
Conflicting
—2
Total16181139117455

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

XYLT1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

3D Protein StructureAlphaFold

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Complete and partial XYLT1 deletion in a patient with neonatal short limb skeletal dysplasia.
van Koningsbruggen S et al.·Am J Med Genet A
2016
Novel compound heterozygous variants in XYLT1 gene caused Desbuquois dysplasia type 2 in an aborted fetus: a case report.
Rajabi F et al.·BMC Pediatr
2022Case report
Prenatal Diagnosis, Ultrasound Findings, and Follow-Up Evaluation of 16p13.11 Deletion and Duplication Syndromes: Preliminary Assessment of Fetal Genotype-Phenotype.
Luo X et al.·J Clin Lab Anal
2025Natural history
Further Defining the Phenotypic Spectrum of B3GAT3 Mutations and Literature Review on Linkeropathy Syndromes.
Ritelli M et al.·Genes (Basel)
2019Review
GGC Repeat Expansion and Exon 1 Methylation of XYLT1 Is a Common Pathogenic Variant in Baratela-Scott Syndrome.
LaCroix AJ et al.·Am J Hum Genet
2019
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients