UPRT

uracil phosphoribosyltransferase homolog

Basic information

Region (hg38): X:75156388-75304885

Links

ENSG00000094841NCBI:139596OMIM:300656HGNC:28334Uniprot:Q96BW1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UPRT 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
5
clinvar
1
clinvar
6
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
1
clinvar
1
clinvar
2
Total 0 0 5 2 1

Variants in UPRT

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

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

Position Type Phenotype Significance ClinVar
X-75156585-C-T Benign (Jun 14, 2018)1260246
X-75274279-G-C not specified Uncertain significance (Sep 28, 2021)2252710
X-75274392-G-C not specified Uncertain significance (Dec 13, 2022)2408492
X-75274427-C-G not specified Likely benign (Jan 04, 2022)2269821
X-75274453-G-A not specified Uncertain significance (Dec 16, 2022)2405224
X-75274469-C-T not specified Conflicting classifications of pathogenicity (Aug 08, 2022)1206381
X-75274636-G-A not specified Uncertain significance (Jul 14, 2024)3466317
X-75300980-A-C Likely benign (Jul 01, 2022)2660945
X-75303443-A-G not specified Uncertain significance (Dec 06, 2022)2333884

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
UPRTprotein_codingprotein_codingENST00000373383 730516
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.5780.420125712021257140.00000795
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.45701130.6170.000007902016
Missense in Polyphen1046.230.21631851
Synonymous0.1934041.60.9620.00000277616
Loss of Function2.55211.20.1789.30e-7177

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.0001450.000109
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.0001450.000109
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Pathway
Pyrimidine metabolism - Homo sapiens (human);Pyrimidine metabolism (Consensus)

Recessive Scores

pRec
0.233

Intolerance Scores

loftool
0.262
rvis_EVS
-0.08
rvis_percentile_EVS
47.79

Haploinsufficiency Scores

pHI
0.106
hipred
Y
hipred_score
0.688
ghis
0.612

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.970

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumLowLow
Primary ImmunodeficiencyMediumLowMedium
CancerMediumLowMedium

Mouse Genome Informatics

Gene name
Uprt
Phenotype

Gene ontology

Biological process
UMP biosynthetic process;female pregnancy;lactation;response to insulin
Cellular component
nucleus;cytoplasm
Molecular function
protein binding;GTP binding;kinase activity