GXYLT1

glucoside xylosyltransferase 1, the group of Glycosyltransferase family 8

Basic information

Region (hg38): 12:42081844-42144874

Previous symbols: [ "GLT8D3" ]

Links

ENSG00000151233 ∙ NCBI:283464 ∙ OMIM:613321 ∙ HGNC:27482 ∙ Uniprot:Q4G148 ∙ 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 GXYLT1 gene.

• not provided (14 variants)
• Inborn genetic diseases (12 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GXYLT1 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				13		13
missense			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	11	15	0

Variants in GXYLT1

This is a list of pathogenic ClinVar variants found in the GXYLT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-42087805-C-G		not specified	Likely benign (Dec 07, 2022)
12-42087815-G-T		not specified	Uncertain significance (Nov 09, 2023)
12-42087829-T-C		not specified	Uncertain significance (Nov 17, 2022)
12-42087943-G-C		not specified	Uncertain significance (Feb 13, 2024)
12-42097488-T-C		not specified	Uncertain significance (Mar 14, 2023)
12-42097540-C-T		not specified	Uncertain significance (Feb 22, 2023)
12-42097543-C-T		not specified	Uncertain significance (Mar 22, 2023)
12-42097577-T-A			Likely benign (Jun 01, 2022)
12-42097994-G-A		not specified	Uncertain significance (Dec 28, 2022)
12-42109629-A-C		not specified	Uncertain significance (Oct 10, 2023)
12-42109653-C-T		GXYLT1-related disorder	Likely benign (Dec 09, 2019)
12-42109665-T-C		GXYLT1-related disorder	Benign (Oct 30, 2019)
12-42109678-G-A		not specified	Uncertain significance (Dec 21, 2022)
12-42109700-AT-A			Likely benign (Dec 28, 2023)
12-42109703-T-TA			Benign (Dec 28, 2023)
12-42119003-G-T			Likely benign (Sep 01, 2023)
12-42129785-C-T		not specified	Uncertain significance (Dec 07, 2021)
12-42129807-A-G		not specified	Uncertain significance (Sep 29, 2023)
12-42129837-G-C		not specified	Uncertain significance (Feb 21, 2024)
12-42144467-G-A			Likely benign (Aug 01, 2023)
12-42144469-C-A		not specified	Uncertain significance (May 24, 2023)
12-42144479-G-T			Likely benign (Aug 01, 2023)
12-42144482-G-A			Likely benign (Aug 01, 2023)
12-42144491-G-T			Likely benign (Aug 01, 2023)
12-42144518-G-A			Likely benign (Aug 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GXYLT1	protein_coding	protein_coding	ENST00000398675	8	63035

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.125	0.875	124753	0	32	124785	0.000128

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.358	190	204	0.929	0.00000980	2823
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000269	0.000269
Ashkenazi Jewish	0.00119	0.00119
East Asian	0.0000584	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000986	0.0000971
Middle Eastern	0.0000584	0.0000556
South Asian	0.0000427	0.0000327
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) (Consensus)

Recessive Scores

• pRec: 0.0917

Intolerance Scores

• loftool: 0.217
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.216
• hipred: N
• hipred_score: 0.413
• ghis: 0.632

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gxylt1

Gene ontology

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