XXYLT1

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

Basic information

Region (hg38): 3:195068283-195271159

Previous symbols: [ "C3orf21" ]

Links

ENSG00000173950 ∙ NCBI:152002 ∙ OMIM:614552 ∙ HGNC:26639 ∙ Uniprot:Q8NBI6 ∙ 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 XXYLT1 gene.

• Inborn genetic diseases (23 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the XXYLT1 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	1

Variants in XXYLT1

This is a list of pathogenic ClinVar variants found in the XXYLT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-195069729-T-C		not specified	Uncertain significance (Dec 21, 2023)
3-195069811-G-T		not specified	Uncertain significance (Dec 28, 2023)
3-195069812-T-G		not specified	Uncertain significance (Nov 30, 2022)
3-195069856-C-T			Benign (Aug 27, 2018)
3-195069936-T-C		not specified	Uncertain significance (Apr 25, 2022)
3-195069939-C-T		not specified	Uncertain significance (Jul 13, 2021)
3-195070052-G-C		not specified	Uncertain significance (Nov 03, 2022)
3-195070058-G-A		not specified	Uncertain significance (Mar 21, 2023)
3-195070096-C-A		not specified	Uncertain significance (Oct 14, 2023)
3-195156471-G-A		not specified	Uncertain significance (Dec 13, 2023)
3-195156489-C-T		not specified	Uncertain significance (Sep 28, 2022)
3-195156494-G-A		not specified	Uncertain significance (Dec 08, 2023)
3-195156527-C-T		not specified	Uncertain significance (Jun 22, 2021)
3-195156528-G-A		not specified	Uncertain significance (Dec 06, 2023)
3-195226778-C-G		not specified	Uncertain significance (May 27, 2022)
3-195226783-C-T		not specified	Uncertain significance (Feb 16, 2023)
3-195226796-G-C		not specified	Uncertain significance (Aug 04, 2023)
3-195226828-G-A		not specified	Uncertain significance (Oct 27, 2022)
3-195270608-C-A		not specified	Uncertain significance (Jan 17, 2024)
3-195270641-G-T		not specified	Uncertain significance (Jun 07, 2023)
3-195270644-G-A		not specified	Uncertain significance (Jul 25, 2023)
3-195270666-G-C		not specified	Uncertain significance (Feb 11, 2022)
3-195270673-G-A		not specified	Uncertain significance (Nov 27, 2023)
3-195270709-T-G		not specified	Uncertain significance (Jul 15, 2021)
3-195270713-C-T		not specified	Uncertain significance (Dec 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
XXYLT1	protein_coding	protein_coding	ENST00000310380	4	202889

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00132	0.872	124656	0	140	124796	0.000561

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.524	189	210	0.898	0.0000124	2513
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000164	0.000158
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000571	0.0000556
Finnish	0.00535	0.00535
European (Non-Finnish)	0.000144	0.000141
Middle Eastern	0.0000571	0.0000556
South Asian	0.0000683	0.0000654
Other	0.000499	0.000495

dbNSFP

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}.

Haploinsufficiency Scores

• pHI: 0.0761
• hipred: N
• hipred_score: 0.468
• ghis: 0.557

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: Xxylt1
• Phenotype: hematopoietic system phenotype; pigmentation phenotype; vision/eye phenotype; immune system phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: O-glycan processing
• Cellular component: integral component of endoplasmic reticulum membrane
• Molecular function: magnesium ion binding;manganese ion binding;UDP-xylosyltransferase activity