RXYLT1

Chr 12AR

ribitol xylosyltransferase 1

Also known as: HP10481, MDDGA10, TMEM5

NCBI Gene: 10329ENSG00000118600UniProt: Q9Y2B1OMIM: 605862

This gene encodes a glycosyltransferase that catalyzes xylose transfer to ribitol 5-phosphate in the biosynthesis of phosphorylated O-mannosyl trisaccharides on alpha-dystroglycan, which are required for binding laminin-containing extracellular proteins. Mutations cause autosomal recessive muscular dystrophy-dystroglycanopathy with congenital brain and eye anomalies, featuring cobblestone lissencephaly. The gene shows low constraint against loss-of-function variants in the population.

OMIMResearchSummary from RefSeq, OMIM, UniProt
LOFmechanismARLOEUF 0.931 OMIM phenotype
Clinical Summary— RXYLT1
🧬
Gene-Disease Validity (ClinGen)
muscle-eye-brain disease · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
29 unique Pathogenic / Likely Pathogenic· 62 VUS of 167 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.93LOEUF
pLI 0.000
Z-score 1.82
OE 0.58 (0.38–0.93)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.73Z-score
OE missense 0.86 (0.77–0.97)
199 obs / 230.2 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.58 (0.38–0.93)
0≤0.351.4
Missense OE0.86 (0.77–0.97)
0≤0.61.4
Synonymous OE0.96
0≤1.21.6
LoF obs/exp: 13 / 22.3Missense obs/exp: 199 / 230.2Syn Z: 0.33

ClinVar Variant Classifications

167 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic19
Likely Pathogenic10
VUS62
Likely Benign59
Benign5
Conflicting4
19
Pathogenic
10
Likely Pathogenic
62
VUS
59
Likely Benign
5
Benign
4
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
12
0
7
0
19
Likely Pathogenic
8
2
0
0
10
VUS
1
59
2
0
62
Likely Benign
0
4
17
38
59
Benign
0
2
2
1
5
Conflicting
—4
Total21672839159

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

View in ClinVar →

Protein Context — Lollipop Plot

RXYLT1 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold
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
Top 1 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

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