UPRT

protein-coding

uracil phosphoribosyltransferase homolog

Gene summary

This gene encodes uracil phosphoribosyltransferase, which catalyzes the conversion of uracil and 5-phosphoribosyl-1-R-diphosphate to uridine monophosphate (UMP). This reaction is an important part of nucleotide metabolism, specifically the pyrimidine salvage pathway. The enzyme localizes to the nucleus and cytoplasm. The protein is a potential target for rational design of drugs to treat parasitic infections and cancer. [provided by RefSeq, Nov 2009]

MANE transcript

NM_145052.4

Inheritance

—

ClinVar variants

U:57B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chrX:75,156,388-75,304,885

External References & Databases

Ensembl (ENSG00000094841)

Transcript & Mutation Effects

hg38 • Region Span ~148.5 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to UPRT variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 14

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_145052.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			10 clinvar			10
missense			32 clinvar	2 clinvar		34
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			14 clinvar			14
Total	0	0	57	2	0	59

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 30 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_145052.4	RefSeq	NP_659489.1	7	MANE Select
ENST00000373383.9	Ensembl	ENSP00000362481.4	7	MANE Select
NM_001307944.1	RefSeq	NP_001294873.1	6	Standard
NM_001363821.1	RefSeq	NP_001350750.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Pyrimidine metabolism - Homo sapiens (human)
Pyrimidine metabolism

Biological Process

UMP biosynthetic process
female pregnancy
lactation
response to insulin

Molecular Function

protein binding
GTP binding
kinase activity

Cellular Component

nucleus
cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000373383
Coding exons: 7
Length: 30516
Individuals with no LoFs: 125712
Homozygous LoFs: 0
Heterozygous LoFs: 2
Defined: 125714
p: 0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.45	70	113	0.617	0.00000790	2016
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00014	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.233

Intolerance Scores

LoFtool: 0.262
RVIS EVS: -0.08
RVIS percentile EVS: 47.79

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.970

Gene Damage Prediction

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