CDA

cytidine deaminase

Basic information

Region (hg38): 1:20589085-20618903

Links

ENSG00000158825 ∙ NCBI:978 ∙ OMIM:123920 ∙ HGNC:1712 ∙ Uniprot:P32320 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

• Inborn genetic diseases (4 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CDA 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					2	2
missense			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	2

Variants in CDA

This is a list of pathogenic ClinVar variants found in the CDA region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
1-20589245-G-C		not specified	Uncertain significance (Nov 17, 2023)
1-20604956-G-A			Benign (Mar 29, 2018)
1-20604983-T-C			Benign (Jul 10, 2018)
1-20605032-A-C		not specified	Uncertain significance (Jul 25, 2023)
1-20613861-A-G		not specified	Uncertain significance (Aug 12, 2021)
1-20618478-G-A		not specified	Uncertain significance (Nov 03, 2023)
1-20618486-C-T		not specified	Uncertain significance (Nov 08, 2022)
1-20618495-C-T		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CDA	protein_coding	protein_coding	ENST00000375071	4	29961

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00810	0.803	125725	0	5	125730	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.297	75	82.6	0.908	0.00000454	950
Missense in Polyphen		26	29.355	0.88571		345
Synonymous	0.872	28	34.5	0.811	0.00000214	279
Loss of Function	1.02	4	6.90	0.580	3.00e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000547	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000901	0.00000879
Middle Eastern	0.0000547	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000166	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: This enzyme scavenges exogenous and endogenous cytidine and 2'-deoxycytidine for UMP synthesis.
• Pathway: Pyrimidine metabolism - Homo sapiens (human);Drug metabolism - other enzymes - Homo sapiens (human);Fluoropyrimidine Pathway, Pharmacokinetics;Gemcitabine Pathway, Pharmacodynamics;Pyrimidine Metabolism;Capecitabine Action Pathway;Capecitabine Metabolism Pathway;UMP Synthase Deiciency (Orotic Aciduria);MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy);Beta Ureidopropionase Deficiency;Dihydropyrimidinase Deficiency;Fluoropyrimidine Activity;pyrimidine ribonucleosides degradation;Pyrimidine metabolism;Neutrophil degranulation;pyrimidine deoxyribonucleosides degradation;Metabolism of nucleotides;Innate Immune System;Immune System;Metabolism;Pyrimidine salvage;Nucleotide salvage;Pyrimidine metabolism;pyrimidine ribonucleosides degradation;superpathway of pyrimidine deoxyribonucleoside salvage;Pyrimidine nucleotides nucleosides metabolism;pyrimidine ribonucleosides salvage I;pyrimidine deoxyribonucleosides salvage (Consensus)

Recessive Scores

• pRec: 0.553

Intolerance Scores

• loftool: 0.229
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.75

Haploinsufficiency Scores

• pHI: 0.191
• hipred: N
• hipred_score: 0.332
• ghis: 0.571

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.808

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Cda

Gene ontology

• Biological process: cell surface receptor signaling pathway;pyrimidine-containing compound salvage;cytidine deamination;cytosine metabolic process;negative regulation of cell growth;pyrimidine nucleoside salvage;neutrophil degranulation;negative regulation of nucleotide metabolic process;protein homotetramerization
• Cellular component: extracellular region;cytosol;secretory granule lumen;tertiary granule lumen;ficolin-1-rich granule lumen
• Molecular function: nucleoside binding;cytidine deaminase activity;protein binding;zinc ion binding;protein homodimerization activity