UXS1
Basic information
Region (hg38): 2:106093308-106194301
Links
Phenotypes
GenCC
Source:
- skeletal dysplasia (Limited), mode of inheritance: AD
ClinVar
This is a list of variants' phenotypes submitted to
- 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 | |||||
missense | 41 | 41 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 0 | 0 | 41 | 1 | 0 |
GnomAD
Source:
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:
- 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