CDO1

cysteine dioxygenase type 1

Basic information

Region (hg38): 5:115804733-115816659

Links

ENSG00000129596

∙ NCBI:1036 ∙ OMIM:603943 ∙ HGNC:1795 ∙ Uniprot:Q16878 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CDO1 gene.

not_specified (20 variants)
not_provided (3 variants)
CDO1-related_disorder (1 variants)

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. These statistics are base on transcript: NM_000001801.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			23 clinvar			23
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	23	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

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: dbNSFP

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