UPRT

uracil phosphoribosyltransferase homolog

Basic information

Region (hg38): X:75156388-75304885

Links

ENSG00000094841 ∙ NCBI:139596 ∙ OMIM:300656 ∙ HGNC:28334 ∙ Uniprot:Q96BW1 ∙ 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 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	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	1	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)
X-75274279-G-C		not specified	Uncertain significance (Sep 28, 2021)
X-75274392-G-C		not specified	Uncertain significance (Dec 13, 2022)
X-75274427-C-G		not specified	Likely benign (Jan 04, 2022)
X-75274453-G-A		not specified	Uncertain significance (Dec 16, 2022)
X-75274469-C-T		not specified	Conflicting classifications of pathogenicity (Aug 08, 2022)
X-75274636-G-A		not specified	Uncertain significance (Jul 14, 2024)
X-75300980-A-C			Likely benign (Jul 01, 2022)
X-75303443-A-G		not specified	Uncertain significance (Dec 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UPRT	protein_coding	protein_coding	ENST00000373383	7	30516

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.578	0.420	125712	0	2	125714	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	70	113	0.617	0.00000790	2016
Missense in Polyphen		10	46.23	0.21631		851
Synonymous	0.193	40	41.6	0.962	0.00000277	616
Loss of Function	2.55	2	11.2	0.178	9.30e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.000145	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000145	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

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

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

Mouse Genome Informatics

• Gene name: Uprt

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