CDO1
cysteine dioxygenase type 1
Basic information
Region (hg38): 5:115804733-115816659
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDO1 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 0 |
Variants in CDO1
This is a list of pathogenic ClinVar variants found in the CDO1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-115806398-T-C | not specified | Uncertain significance (May 11, 2022) | ||
| 5-115806456-A-T | not specified | Uncertain significance (May 24, 2024) | ||
| 5-115811236-G-C | not specified | Uncertain significance (Jun 06, 2023) | ||
| 5-115813260-T-TA | CDO1-related disorder | Likely benign (Apr 19, 2021) | ||
| 5-115816231-T-C | not specified | Uncertain significance (Aug 09, 2021) | ||
| 5-115816247-C-A | not specified | Uncertain significance (Nov 08, 2022) | ||
| 5-115816309-A-G | not specified | Uncertain significance (Oct 27, 2022) | ||
| 5-115816313-T-C | not specified | Uncertain significance (Feb 22, 2023) | ||
| 5-115816352-T-C | not specified | Uncertain significance (Jan 30, 2024) | ||
| 5-115816374-C-A | not specified | Uncertain significance (Dec 15, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| CDO1 | protein_coding | protein_coding | ENST00000250535 | 5 | 12222 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00966 | 0.946 | 125740 | 0 | 8 | 125748 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.190 | 104 | 110 | 0.949 | 0.00000505 | 1340 |
| Missense in Polyphen | 67 | 65.08 | 1.0295 | 833 | ||
| Synonymous | 1.28 | 30 | 40.3 | 0.744 | 0.00000193 | 353 |
| Loss of Function | 1.74 | 5 | 11.3 | 0.441 | 6.31e-7 | 119 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000909 | 0.0000904 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000944 | 0.0000924 |
| European (Non-Finnish) | 0.0000267 | 0.0000264 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000334 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Initiates several important metabolic pathways related to pyruvate and several sulfurate compounds including sulfate, hypotaurine and taurine. Critical regulator of cellular cysteine concentrations. Has an important role in maintaining the hepatic concentation of intracellular free cysteine within a proper narrow range.;
- Pathway
- Cysteine and methionine metabolism - Homo sapiens (human);Taurine and hypotaurine metabolism - Homo sapiens (human);Beta-mercaptolactate-cysteine disulfiduria;Cysteine Metabolism;Taurine and Hypotaurine Metabolism;Cystinosis, ocular nonnephropathic;HH-Ncore;One carbon metabolism and related pathways;taurine biosynthesis;Degradation of cysteine and homocysteine;Metabolism of amino acids and derivatives;Glycine Serine metabolism;L-cysteine degradation I;Metabolism;Methionine Cysteine metabolism;Methionine and cysteine metabolism;Sulfur amino acid metabolism;superpathway of methionine degradation
(Consensus)
Recessive Scores
- pRec
- 0.243
Intolerance Scores
- loftool
- 0.750
- rvis_EVS
- -0.16
- rvis_percentile_EVS
- 41.25
Haploinsufficiency Scores
- pHI
- 0.250
- hipred
- N
- hipred_score
- 0.444
- ghis
- 0.534
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Cdo1
- Phenotype
- growth/size/body region phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; vision/eye phenotype;
Gene ontology
- Biological process
- sulfur amino acid biosynthetic process;cysteine metabolic process;inflammatory response;lactation;L-cysteine catabolic process;response to glucagon;taurine biosynthetic process;response to amino acid;response to ethanol;response to glucocorticoid;response to cAMP;oxidation-reduction process
- Cellular component
- cytosol
- Molecular function
- ferrous iron binding;cysteine dioxygenase activity