GXYLT2

glucoside xylosyltransferase 2, the group of Glycosyltransferase family 8

Basic information

Region (hg38): 3:72888046-72998138

Previous symbols: [ "GLT8D4" ]

Links

ENSG00000172986 ∙ NCBI:727936 ∙ OMIM:613322 ∙ HGNC:33383 ∙ Uniprot:A0PJZ3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GXYLT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GXYLT2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			31		1	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	31	0	2

Variants in GXYLT2

This is a list of pathogenic ClinVar variants found in the GXYLT2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-72888246-A-G		not specified	Uncertain significance (Sep 26, 2024)
3-72888248-C-G		not specified	Uncertain significance (Aug 02, 2021)
3-72888279-G-T		not specified	Uncertain significance (Nov 20, 2023)
3-72888280-C-T		not specified	Uncertain significance (Jul 07, 2024)
3-72888330-C-G		not specified	Uncertain significance (Nov 22, 2022)
3-72888348-C-T		not specified	Uncertain significance (Sep 30, 2024)
3-72888378-C-A		not specified	Uncertain significance (Jan 23, 2023)
3-72888378-C-T		not specified	Uncertain significance (Jan 17, 2024)
3-72888397-C-T		not specified	Uncertain significance (Mar 16, 2024)
3-72888399-G-A		not specified	Uncertain significance (Mar 16, 2022)
3-72888442-G-T		not specified	Uncertain significance (Jun 17, 2022)
3-72888444-C-T		not specified	Uncertain significance (Sep 14, 2023)
3-72888505-C-T		not specified	Uncertain significance (May 18, 2023)
3-72908419-A-C		not specified	Uncertain significance (Aug 14, 2024)
3-72908531-A-T		not specified	Uncertain significance (Jun 27, 2022)
3-72922207-C-T		not specified	Uncertain significance (Nov 16, 2021)
3-72922208-G-A		not specified	Uncertain significance (Dec 14, 2021)
3-72922258-A-G			Benign (Feb 09, 2018)
3-72922262-C-G		not specified	Uncertain significance (Jul 06, 2021)
3-72922263-A-G			Benign (Feb 09, 2018)
3-72922334-C-T		not specified	Uncertain significance (Feb 16, 2023)
3-72955170-A-T		not specified	Uncertain significance (Dec 01, 2022)
3-72955198-C-G		not specified	Uncertain significance (Jul 07, 2022)
3-72955215-A-G		not specified	Uncertain significance (Aug 11, 2022)
3-72955225-A-G		not specified	Uncertain significance (Oct 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GXYLT2	protein_coding	protein_coding	ENST00000389617	7	110066

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.37e-14	0.0147	124598	1	44	124643	0.000181

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.408	186	202	0.919	0.0000110	2855
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000184
Ashkenazi Jewish	0.00	0.00
East Asian	0.000335	0.000334
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000160	0.000159
Middle Eastern	0.000335	0.000334
South Asian	0.000458	0.000425
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Other types of O-glycan biosynthesis - Homo sapiens (human);Vitamin D Receptor Pathway (Consensus)

Intolerance Scores

• loftool: 0.690
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.74

Haploinsufficiency Scores

• pHI: 0.197
• hipred: N
• hipred_score: 0.238
• ghis: 0.532

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gxylt2

Gene ontology

• Biological process: O-glycan processing
• Cellular component: integral component of membrane
• Molecular function: UDP-xylosyltransferase activity