UROS

protein-coding

uroporphyrinogen III synthase

Gene summary

The protein encoded by this gene catalyzes the fourth step of porphyrin biosynthesis in the heme biosynthetic pathway. Defects in this gene cause congenital erythropoietic porphyria (Gunther's disease). [provided by RefSeq, Jul 2008]

MANE transcript

NM_000375.3

Inheritance

AR

ClinVar variants

P:26U:46B:29

Top phenotype

Porphyria, congenital erythropoietic

gnomAD constraint

pLI —, LoF o/e 0.35

Max pathogenic AF

—

Genomic locus

chr10:125,784,980-125,823,288

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~38.3 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

cutaneous porphyriaSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009902

Submitter: Orphanet

cutaneous porphyriaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009902

Submitter: Labcorp Genetics (formerly Invitae)

cutaneous porphyriaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009902

Submitter: PanelApp Australia

cutaneous porphyriaDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009902

Submitter: ClinGen

The gene *UROS* has been definitively associated with the gene-disease relationship of UROS-related porphyria also known as congenital erythropoietic porphyria (CEP) according to the gene-disease validity curation process (Standard Operating Procedures Version 11) of the ACMG. UROS (uroporphyrinogen-III synthase) is a cytosolic enzyme and the fourth step in the heme synthesis pathway. It catalyzes the cyclization of the linear substrate hydroxymethylbilane into uroporphyrinogen III. When UROS activity is reduced, hydroxymethylbilane can spontaneously cyclize into uroporphyrinogen I isomers. Although these isomers, like uroporphyrinogen III, are substrates for the next enzyme in the pathway, UROD (Uroporphyrinogen decarboxylase), the products, coproporphyrinogen I isomers are not a substrate for the subsequent enzyme, CPOX (coproporphyrinogen-III oxidase), in heme synthesis. As a result, the non enzymatically produced uroporphyrinogen I isomers represent a dead end in the pathway (PMID: 19268002). UROS-related porphyria, like other porphyrias, shows phenotypic variability ranging from mild to severe, with the severity generally correlating with the degree of reduced enzymatic activity. But unlike the semidominant porphyria, PPOX-related variegate porphyria where severe symptoms present at <25% WT enzyme activity, autosomal recessive UROS-related porphyria must have homozygous or biallelic mutations that nearly abolish enzyme function <5% before severe disease manifests. Mutations causing this disease are found throughout the UROS exons and in the promoter region. A common severe presentation is caused by homozygosity for the p.C73R mutation, resulting in less than 1-2% enzymatic activity (PMID: 19268002). Affected individuals may present in utero with non-immune hydrops fetalis due to hemolytic anemia. If they survive infancy, they experience extreme photosensitivity, often leading to disfigurement from severe scarring. Hemolysis is common, and additional described symptoms include red-wine-colored urine, erythrodontia (red-brown-stained teeth), splenomegaly, scleromalacia, and chronic ulcerative keratitis. Biochemical phenotypes include elevated urinary porphyrins (particularly massive amounts of uroporphyrin I), fecal porphyrins, and plasma porphyrins. In the blood, erythrocytes show polychromasia, poikilocytosis, anisocytosis, and basophilic stippling, along with an increase in reticulocytes and nucleated red blood cells. The only known cure for severe disease is bone marrow transplantation which is required as early as possible after birth, to improve chances of its effectiveness (PMID: 30594473, PMID: 31326287). For biallelic heterozygotes if enzyme activity is <5%, severe disease often results, but for activity levels between 5-12% of WT mild to moderate disease occurs. Mild to moderate disease may have later onset and symptoms are usually cutaneous photosensitivity which often presents as bullous skin lesions, hypo- or hyperpigmentation of the affected skin, and recurrent skin infections (PMID: 19268002). Summary of Case Level Data (12 points): 14 probands were scored with 15 unique variants (two splicing mutations, three promoter mutations and ten missense variants in exons). All of the variants scored have been characterized in *E. coli* for their relative enzymatic activity compared to WT. Summary of Experimental Evidence (2.5 points): Biochemical characterization of the enzymatic reaction was scored (.5 pts). A knock-in mouse model for the P248Q missense mutation reproducing the phenotypes of erythrodontia, moderate photosensitivity, hepatosplenomegaly, and hemolytic anemia was scored at 2 points. In summary, UROS has been definitively associated with autosomal recessive UROS-related porphyria.

cutaneous porphyriaSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0009902

Submitter: Genomics England PanelApp

cutaneous porphyriaDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0009902

Submitter: G2P

Clinical Genomic Database (CGD)

Porphyria, congenital erythropoieticAR

Manifestation: Dermatologic; Hematologic

Intervention: Dermatologic; Hematologic

Rationale: Transfusions can be beneficial; Individuals can prevent with bleeding diatheses, and prompt treatment may be beneficial; Limitation to sun exposure may be beneficial due ot photosensitivity; Manifestations such as thrombocytopenia and hemolytic anemia, may be effectively treated by splenectomy; Use of oral sorbents have been described; BMT has been described in severe cases

Refs: 7205063; 3960070; 3100953; 2331520; 2207013; 8829650; 9834209; 12060112; 15703981; 22090724; 22350154; 22816431; 23557135; 23626549Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to UROS variants in ClinVar

5 Conditions Cataloged
not providedTotal: 77
Cutaneous porphyriaTotal: 44
Inborn genetic diseasesTotal: 28
UROS-related disorderTotal: 12
not specifiedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000375.3. 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.

EffectPLPVUSLBBSum
synonymous
18
clinvar
3
clinvar
21
missense
14
clinvar
4
clinvar
42
clinvar
7
clinvar
1
clinvar
68
nonsense
2
clinvar
2
start loss
0
frameshift
2
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
3
clinvar
4
clinvar
8
Total19746254101

Highest pathogenic variant AF is 0.00026514355

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 113 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_000375.3RefSeqNP_000366.19MANE Select
ENST00000368797.10EnsemblENSP00000357787.49MANE Select
NM_001324036.2RefSeqNP_001310965.110Standard
NM_001324037.2RefSeqNP_001310966.19Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Porphyrin and chlorophyll metabolism - Homo sapiens (human)
  • Hereditary Coproporphyria (HCP)
  • Porphyria Variegata (PV)
  • Congenital Erythropoietic Porphyria (CEP) or Gunther Disease
  • Acute Intermittent Porphyria

Biological Process

  • uroporphyrinogen III biosynthetic process
  • protoporphyrinogen IX biosynthetic process
  • heme biosynthetic process

Molecular Function

  • uroporphyrinogen-III synthase activity

Cellular Component

  • mitochondrion
  • cytosol

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000368797
Coding exons
9
Length
34672
Individuals with no LoFs
125729
Homozygous LoFs
0
Heterozygous LoFs
19
Defined
125748
p
0.0000756
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.08171421391.020.000007151707
Missense (PolyPhen)4956.6510.86494644
Synonymous0.3205558.10.9470.00000356515
Loss of Function2.31514.50.3456.15e-7194

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000310.00031rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.000110.00011rare
South Asian0.0000650.000065rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Catalyzes cyclization of the linear tetrapyrrole, hydroxymethylbilane, to the macrocyclic uroporphyrinogen III, the branch point for the various sub-pathways leading to the wide diversity of porphyrins. Porphyrins act as cofactors for a multitude of enzymes that perform a variety of processes within the cell such as methionine synthesis (vitamin B12) or oxygen transport (heme).;
Disease
DISEASE: Note=Severe congenital erythropoietic porphyria is associated with non-immune hydrops fetalis, a generalized edema of the fetus with fluid accumulation in the body cavities due to non- immune causes. Non-immune hydrops fetalis is not a diagnosis in itself but a symptom, a feature of many genetic disorders, and the end-stage of a wide variety of disorders.;

Recessive Scores

pRec
0.102

Intolerance Scores

LoFtool
0.173
RVIS EVS
-0.1
RVIS percentile EVS
46.49

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
S
Essential (gene trap)
N
Indispensability pred.
E
Indispensability score
0.996

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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