XXYLT1

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

Basic information

Region (hg38): 3:195068284-195271159

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.

not_specified (75 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. These statistics are base on transcript: NM_000152531.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					1 clinvar	1
missense			74 clinvar	1 clinvar		75
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	74	1	1

Loading clinvar variants...

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