GXYLT2

protein-coding

glucoside xylosyltransferase 2, the group of Glycosyltransferase family 8

Gene summary

The protein encoded by this gene is a xylosyltransferase that elongates O-linked glucose bound to epidermal growth factor (EGF) repeats. The encoded protein catalyzes the addition of xylose to the O-glucose-modified residues of EGF repeats of Notch proteins. [provided by RefSeq, Sep 2016]

Previous symbols:

GLT8D4

MANE transcript

NM_001080393.2

Inheritance

—

ClinVar variants

U:83B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.04

Max pathogenic AF

—

Genomic locus

chr3:72,888,046-72,998,138

External References & Databases

Ensembl (ENSG00000172986)

Transcript & Mutation Effects

hg38 • Region Span ~110.1 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 GXYLT2 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 81

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001080393.2. 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			1 clinvar		1 clinvar	2
missense			81 clinvar	1 clinvar	1 clinvar	83
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	83	1	2	86

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 7 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001080393.2	RefSeq	NP_001073862.1	7	MANE Select
ENST00000389617.9	Ensembl	ENSP00000374268.4	7	MANE Select
ENST00000491839.1	Ensembl	ENSP00000420426.1	4	Standard
ENST00000498315.1	Ensembl	ENSP00000417239.1	3	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)
Vitamin D Receptor Pathway

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: ENST00000389617
Coding exons: 7
Length: 110066
Individuals with no LoFs: 124598
Homozygous LoFs: 1
Heterozygous LoFs: 44
Defined: 124643
p: 0.000181

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.408	186	202	0.919	0.0000110	2855
Missense (PolyPhen)		88	107.23	0.82068		1241
Synonymous	0.662	71	78.5	0.905	0.00000467	888
Loss of Function	-0.144	20	19.3	1.04	0.00000101	234

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00033	0.00033	rare
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00046	0.00042	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}.;

Intolerance Scores

LoFtool: 0.690
RVIS EVS: 0.06
RVIS percentile EVS: 58.74

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