XXYLT1

protein-coding

xyloside xylosyltransferase 1, the group of Glycosyltransferase family 8|MicroRNA protein coding host genes

Gene summary

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]

Previous symbols:

C3orf21

MANE transcript

NM_152531.5

Inheritance

—

ClinVar variants

U:86B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.56

Max pathogenic AF

—

Genomic locus

chr3:195,068,284-195,271,159

External References & Databases

Ensembl (ENSG00000173950)

Transcript & Mutation Effects

hg38 • Region Span ~202.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to XXYLT1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 85

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_152531.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			85 clinvar	1 clinvar		86
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	86	1	1	88

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152531.5	RefSeq	NP_689744.3	4	MANE Select
ENST00000310380.11	Ensembl	ENSP00000309640.6	4	MANE Select
NM_001308069.2	RefSeq	NP_001294998.1	4	Standard
NM_001410854.1	RefSeq	NP_001397783.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

O-glycan processing

Molecular Function

magnesium ion binding
manganese ion binding
UDP-xylosyltransferase activity

Cellular Component

integral component of endoplasmic reticulum membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000310380
Coding exons: 4
Length: 202889
Individuals with no LoFs: 124656
Homozygous LoFs: 0
Heterozygous LoFs: 140
Defined: 124796
p: 0.000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.524	189	210	0.898	0.0000124	2513
Missense (PolyPhen)		66	77.192	0.85501		867
Synonymous	1.41	78	95.6	0.816	0.00000614	804
Loss of Function	1.32	6	10.7	0.563	4.55e-7	139

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00013	0.00013	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000057	0.000056	rare
Finnish	0.0053	0.0053	notable
European (Non-Finnish)	0.00014	0.00014	rare
South Asian	0.000068	0.000065	rare
Other	0.00050	0.00050	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Alpha-1,3-xylosyltransferase, which elongates the O- linked xylose-glucose disaccharide attached to EGF-like repeats in the extracellular domain of target proteins by catalyzing the addition of the second xylose (PubMed:22117070, PubMed:8982869). Known targets include Notch proteins and coagulation factors, such as F9 (PubMed:22117070, PubMed:8982869). {ECO:0000269|PubMed:22117070, ECO:0000269|PubMed:8982869}.;

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium