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.

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.

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						0
missense			27			27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	27	0	0

Variants in UXS1

This is a list of pathogenic ClinVar variants found in the UXS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-106094036-C-T		not specified	Uncertain significance (Dec 28, 2022)
2-106094049-T-G		not specified	Uncertain significance (Nov 16, 2021)
2-106098754-G-C		not specified	Uncertain significance (Oct 06, 2021)
2-106098754-G-T		not specified	Uncertain significance (Jan 26, 2025)
2-106098758-G-A		not specified	Uncertain significance (Oct 04, 2024)
2-106101090-T-C		not specified	Uncertain significance (Dec 19, 2022)
2-106101102-G-A		not specified	Uncertain significance (May 13, 2024)
2-106101117-C-T		not specified	Uncertain significance (Jul 14, 2021)
2-106104831-C-T		not specified	Uncertain significance (Feb 13, 2025)
2-106112660-C-G		not specified	Uncertain significance (Jan 26, 2025)
2-106112716-C-T		not specified	Uncertain significance (Feb 23, 2023)
2-106112720-G-A		not specified	Uncertain significance (Mar 12, 2025)
2-106112763-T-G		not specified	Uncertain significance (Sep 28, 2021)
2-106122984-C-A		not specified	Uncertain significance (Feb 02, 2025)
2-106123020-C-T		not specified	Uncertain significance (May 28, 2024)
2-106123032-G-A		not specified	Uncertain significance (Oct 05, 2021)
2-106125650-G-C		not specified	Uncertain significance (Aug 28, 2023)
2-106125655-C-T		not specified	Uncertain significance (Jul 21, 2021)
2-106125656-G-A		not specified	Uncertain significance (Aug 26, 2022)
2-106129701-T-C		not specified	Uncertain significance (Aug 08, 2023)
2-106145232-C-T		not specified	Uncertain significance (Dec 05, 2024)
2-106145262-C-T		not specified	Uncertain significance (Feb 16, 2023)
2-106145312-C-T		not specified	Uncertain significance (Nov 06, 2023)
2-106164738-C-G		not specified	Uncertain significance (Mar 13, 2023)
2-106164771-T-C		not specified	Uncertain significance (Jun 09, 2022)

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