UXS1

UDP-glucuronate decarboxylase 1, the group of Short chain dehydrogenase/reductase superfamily

Basic information

Region (hg38): 2:106093308-106194301

Links

ENSG00000115652

∙ NCBI:80146 ∙ OMIM:609749 ∙ HGNC:17729 ∙ Uniprot:Q8NBZ7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

skeletal dysplasia (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UXS1 gene.

not_specified (42 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UXS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001253875.2. 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			41 clinvar			41
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	41	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UXS1	protein_coding	protein_coding	ENST00000283148	15	101037

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00294	0.997	124645	0	15	124660	0.0000602

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.09	148	239	0.620	0.0000143	2776
Missense in Polyphen		52	109.8	0.47358		1154
Synonymous	-0.368	96	91.5	1.05	0.00000634	766
Loss of Function	3.05	9	25.7	0.351	0.00000134	307

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000592	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000740	0.0000708
Middle Eastern	0.0000592	0.0000556
South Asian	0.000131	0.000131
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the NAD-dependent decarboxylation of UDP- glucuronic acid to UDP-xylose. Necessary for the biosynthesis of the core tetrasaccharide in glycosaminoglycan biosynthesis.;
Pathway: Amino sugar and nucleotide sugar metabolism - Homo sapiens (human);Galactosemia III;Galactosemia II (GALK);Nucleotide Sugars Metabolism;UDP-D-xylose and UDP-D-glucuronate biosynthesis (Consensus)

Recessive Scores

pRec: 0.147

Intolerance Scores

loftool: 0.601
rvis_EVS: -0.56
rvis_percentile_EVS: 19.31

Haploinsufficiency Scores

pHI: 0.198
hipred: Y
hipred_score: 0.685
ghis: 0.611

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.879

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Uxs1
Phenotype: immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Zebrafish Information Network

Gene name: uxs1
Affected structure: chondrocyte
Phenotype tag: abnormal
Phenotype quality: morphology

Gene ontology

Biological process: UDP-D-xylose biosynthetic process;protein tetramerization
Cellular component: cytoplasm;integral component of membrane;Golgi cisterna membrane;extracellular exosome
Molecular function: protein homodimerization activity;UDP-glucuronate decarboxylase activity;NAD+ binding