GXYLT1

protein-coding

glucoside xylosyltransferase 1, the group of Glycosyltransferase family 8

Gene summary

GXYLT1 is a xylosyltransferase (EC 2.4.2.-) that adds the first xylose to O-glucose-modified residues in the epidermal growth factor (EGF; MIM 131530) repeats of proteins such as NOTCH1 (MIM 190198) (Sethi et al., 2010 [PubMed 19940119]).[supplied by OMIM, Mar 2010]

Previous symbols:

GLT8D3

MANE transcript

NM_173601.2

Inheritance

—

ClinVar variants

U:57B:15

Top phenotype

GXYLT1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr12:42,081,845-42,144,874

External References & Databases

Ensembl (ENSG00000151233)

Transcript & Mutation Effects

hg38 • Region Span ~63.0 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 GXYLT1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 51

not providedTotal: 13

GXYLT1-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173601.2. 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			2 clinvar	13 clinvar		15
missense			52 clinvar	2 clinvar		54
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	57	15	0	72

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_173601.2	RefSeq	NP_775872.1	8	MANE Select
ENST00000398675.8	Ensembl	ENSP00000381666.3	8	MANE Select
NM_001099650.2	RefSeq	NP_001093120.1	7	Standard
ENST00000280876.6	Ensembl	ENSP00000280876.6	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Other types of O-glycan biosynthesis - Homo sapiens (human)

Biological Process

O-glycan processing

Molecular Function

UDP-xylosyltransferase activity

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000398675
Coding exons: 8
Length: 63035
Individuals with no LoFs: 124753
Homozygous LoFs: 0
Heterozygous LoFs: 32
Defined: 124785
p: 0.000128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.358	190	204	0.929	0.00000980	2823
Missense (PolyPhen)		76	90.106	0.84345		1214
Synonymous	-0.816	81	72.2	1.12	0.00000352	801
Loss of Function	3.26	6	22.8	0.263	0.00000136	263

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.00020	0.00017	rare
Ashkenazi Jewish	0.0012	0.0012	notable
East Asian	0.000058	0.000056	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000099	0.000097	rare
South Asian	0.000043	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Glycosyltransferase which elongates the O-linked glucose attached to EGF-like repeats in the extracellular domain of Notch proteins by catalyzing the addition of xylose. {ECO:0000269|PubMed:19940119}.;

Recessive Scores

pRec: 0.0917

Intolerance Scores

LoFtool: 0.217
RVIS EVS: -0.25
RVIS percentile EVS: 35.42

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.731

Gene Damage Prediction

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