ODC1
protein-codingornithine decarboxylase 1, the group of Small nucleolar RNA protein coding host genes
Gene summary
This gene encodes the rate-limiting enzyme of the polyamine biosynthesis pathway which catalyzes ornithine to putrescine. The activity level for the enzyme varies in response to growth-promoting stimuli and exhibits a high turnover rate in comparison to other mammalian proteins. Originally localized to both chromosomes 2 and 7, the gene encoding this enzyme has been determined to be located on 2p25, with a pseudogene located on 7q31-qter. Multiple alternatively spliced transcript variants encoding distinct isoforms have been identified. [provided by RefSeq, Dec 2013]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.4 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0033642
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0033642
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0033642
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Dermatologic; Musculoskeletal; Neurologic
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to ODC1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002539.3. 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 | 1 | 9 | 10 | |||
| missense | 48 | 25 | 1 | 74 | ||
| nonsense | 2 | 2 | 1 | 5 | ||
| start loss | 0 | |||||
| frameshift | 2 | 4 | 4 | 10 | ||
| splice donor/acceptor (+/-2bp) | 2 | 5 | 7 | |||
| Total | 6 | 6 | 59 | 34 | 1 | 106 |
Highest pathogenic variant AF is 6.840778e-7
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002530.1 | 10 | MANE Select | |
| Ensembl | ENSP00000234111.4 | 10 | MANE Select | |
| RefSeq | NP_001274117.1 | 8 | Standard | |
| RefSeq | NP_001274118.1 | 10 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| odc1 | Danio rerio | Structure: head Quality: decreased size abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Arginine and proline metabolism - Homo sapiens (human)
- Glutathione metabolism - Homo sapiens (human)
- Spermidine and Spermine Biosynthesis
- Integrated Breast Cancer Pathway
- Methionine De Novo and Salvage Pathway
Biological Process
- kidney development
- regulation of cellular amino acid metabolic process
- polyamine metabolic process
- positive regulation of cell population proliferation
- response to virus
Molecular Function
- ornithine decarboxylase activity
- protein binding
- protein homodimerization activity
Cellular Component
- cellular_component
- cytoplasm
- cytosol
- perinuclear region of cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000234111
- Coding exons
- 10
- Length
- 8537
- Individuals with no LoFs
- 125737
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11
- Defined
- 125748
- p
- 0.0000437
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.47 | 209 | 278 | 0.752 | 0.0000157 | 3064 |
| Missense (PolyPhen) | 41 | 80.268 | 0.51079 | 1027 | ||
| Synonymous | -0.946 | 118 | 106 | 1.12 | 0.00000664 | 862 |
| Loss of Function | 3.02 | 5 | 19.4 | 0.258 | 8.12e-7 | 260 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000035 | 0.000035 | rare |
| South Asian | 0.000034 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Catalyzes the first and rate-limiting step of polyamine biosynthesis that converts ornithine into putrescine, which is the precursor for the polyamines, spermidine and spermine. Polyamines are essential for cell proliferation and are implicated in cellular processes, ranging from DNA replication to apoptosis. {ECO:0000269|PubMed:17900240}.;
Recessive Scores
- pRec
- 0.398
Intolerance Scores
- LoFtool
- 0.147
- RVIS EVS
- -0.45
- RVIS percentile EVS
- 24.33
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |