UROS
protein-codinguroporphyrinogen 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
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~38.3 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0009902
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0009902
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0009902
Submitter: PanelApp Australia
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.
Inheritance Pattern: AR
Disease ID:MONDO:0009902
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0009902
Submitter: G2P
Clinical Genomic Database (CGD)
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
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to UROS variants in ClinVar
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.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 18 | 3 | 21 | |||
| missense | 14 | 4 | 42 | 7 | 1 | 68 |
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 2 | 2 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 3 | 4 | 8 | ||
| Total | 19 | 7 | 46 | 25 | 4 | 101 |
Highest pathogenic variant AF is 0.00026514355
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000366.1 | 9 | MANE Select | |
| Ensembl | ENSP00000357787.4 | 9 | MANE Select | |
| RefSeq | NP_001310965.1 | 10 | Standard | |
| RefSeq | NP_001310966.1 | 9 | Standard |
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:
- 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-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0817 | 142 | 139 | 1.02 | 0.00000715 | 1707 |
| Missense (PolyPhen) | 49 | 56.651 | 0.86494 | 644 | ||
| Synonymous | 0.320 | 55 | 58.1 | 0.947 | 0.00000356 | 515 |
| Loss of Function | 2.31 | 5 | 14.5 | 0.345 | 6.15e-7 | 194 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00011 | 0.00011 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- 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
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |