XXYLT1

Chr 3

xyloside xylosyltransferase 1

Also known as: C3orf21

NCBI Gene: 152002 ENSG00000173950 UniProt: Q8NBI6

Enables magnesium ion binding activity; manganese ion binding activity; and xylosyl alpha-1,3-xylosyltransferase activity. Involved in protein O-linked glycosylation via glucose. Located in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Jun 2026]

Research

ResearchGenerating clinical summary…

Active trials

Pubs (1 yr)

—

P/LP submissions

—

P/LP missense

1.11

LOEUF

Mechanism· predicted

Some data sources returned errors (1)

omim: Error: OMIM fetch failed: 429

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.11LOEUF

pLI 0.001

Z-score 1.32

OE 0.56 (0.31–1.11)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

0.52Z-score

OE missense 0.90 (0.80–1.01)

189 obs / 210.4 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.56 (0.31–1.11)

0≤0.351.4

Missense OE?0.90 (0.80–1.01)

0≤0.61.4

Synonymous OE?0.82

0≤1.21.6

LoF obs/exp: 6 / 10.7Missense obs/exp: 189 / 210.4Syn Z: 1.41

Background carrier burden — how many people carry a rare variant somewhere in XXYLT1?

gnomAD v4 · ~731k individuals · PASS only

Rare means allele frequency under

Rare missense

1 in 71

649 rare PASS variants

Rare truncating (LoF)

1 in 910

87 rare PASS variants

Rare synonymous (reference)

1 in 98

304 rare PASS variants

Truncating variants are far rarer here than missense — that gap, in human units, is what constraint means for XXYLT1. A background rate for each class, not the frequency of any particular variant; thin-coverage exons undercount.

By genetic ancestry · 9 gnomAD groups · rare = under 0.1% in that group

Group	People	Missense	Truncating
European (non-Finnish)	~556k	1 in 90	1 in 1,400
South Asian	~43k	1 in 96	1 in 1,400
Remaining (unassigned)	~30k	1 in 68	1 in 1,400
European (Finnish)	~27k	1 in 200	1 in 1,600
Admixed American	~22k	1 in 83	1 in 1,300
African / African American	~21k	1 in 69	1 in 1,700
East Asian	~20k	1 in 120	1 in 1,300
Ashkenazi Jewish	~13k	1 in 430	none seen
Middle Eastern	~2,884	1 in 100	none seen

Each group is summed over the variants that are rare in that group. Grey ≈ figures rest on fewer than five expected carriers — too few to distinguish groups. Differences mostly reflect how many people were sampled and how much variation each ancestry carries, not disease risk.

Exome coverage (gnomAD): 3 of 4 coding exons well covered in gnomAD exomes; exon 1 marginal. Genomes: all 4.? see exons ↓