DDO

D-aspartate oxidase

Basic information

Region (hg38): 6:110391771-110415575

Links

ENSG00000203797 ∙ NCBI:8528 ∙ OMIM:124450 ∙ HGNC:2727 ∙ Uniprot:Q99489 ∙ 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 DDO gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DDO 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				1		1
missense			22	2		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			4			4
Total	0	0	26	3	0

Variants in DDO

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

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

Position	Type	Phenotype	Significance	ClinVar
6-110392801-T-C		not specified	Uncertain significance (Jul 14, 2021)
6-110392873-C-A		not specified	Uncertain significance (Feb 07, 2023)
6-110392887-C-G		not specified	Uncertain significance (Feb 17, 2022)
6-110392918-C-T		not specified	Uncertain significance (Nov 17, 2023)
6-110392952-G-A			Likely benign (Jul 05, 2018)
6-110393112-T-C		not specified	Uncertain significance (Dec 28, 2023)
6-110393133-T-C		not specified	Uncertain significance (Jan 23, 2024)
6-110393166-T-C		not specified	Uncertain significance (Oct 09, 2024)
6-110393179-C-G		not specified	Uncertain significance (Jun 11, 2024)
6-110393208-G-A		not specified	Uncertain significance (Dec 13, 2021)
6-110393224-C-T		not specified	Uncertain significance (Sep 18, 2024)
6-110393226-C-T		not specified	Uncertain significance (Dec 01, 2022)
6-110393234-C-G		not specified	Uncertain significance (Feb 14, 2024)
6-110393247-A-G		not specified	Uncertain significance (Nov 13, 2024)
6-110393266-C-T		not specified	Uncertain significance (Dec 13, 2023)
6-110393313-G-A		not specified	Uncertain significance (Dec 28, 2023)
6-110393339-T-C		not specified	Uncertain significance (Sep 24, 2024)
6-110404798-G-A		not specified	Uncertain significance (Apr 27, 2024)
6-110404819-G-A		not specified	Uncertain significance (Aug 14, 2024)
6-110404829-C-T		not specified	Uncertain significance (Apr 20, 2024)
6-110404840-A-C		not specified	Uncertain significance (Sep 14, 2023)
6-110404865-C-T		not specified	Uncertain significance (Mar 25, 2024)
6-110404876-A-C		not specified	Uncertain significance (Jul 26, 2022)
6-110404876-A-G		not specified	Uncertain significance (Dec 28, 2023)
6-110404927-G-A		not specified	Uncertain significance (Apr 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DDO	protein_coding	protein_coding	ENST00000368924	5	23792

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.40e-10	0.279	125653	1	94	125748	0.000378

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.425	226	209	1.08	0.0000107	2379
Missense in Polyphen		78	77.44	1.0072		895
Synonymous	-1.51	103	85.3	1.21	0.00000498	774
Loss of Function	0.761	16	19.6	0.815	0.00000143	167

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000925	0.000925
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000371	0.000369
Middle Eastern	0.00	0.00
South Asian	0.000817	0.000784
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Selectively catalyzes the oxidative deamination of D- aspartate and its N-methylated derivative, N-methyl D-aspartate.
• Pathway: Alanine, aspartate and glutamate metabolism - Homo sapiens (human);Peroxisome - Homo sapiens (human);Hypoacetylaspartia;Aspartate Metabolism;Canavan Disease;Alanine Aspartate Asparagine metabolism;Metabolism of proteins;Metabolism of amino acids and derivatives;Metabolism;Peroxisomal protein import;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Glyoxylate metabolism and glycine degradation (Consensus)

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.387
• rvis_EVS: 2.25
• rvis_percentile_EVS: 98.2

Haploinsufficiency Scores

• pHI: 0.0552
• hipred: N
• hipred_score: 0.190

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.933

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ddo
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: aspartate metabolic process;aspartate catabolic process;protein targeting to peroxisome;insemination;grooming behavior;D-amino acid catabolic process;cellular nitrogen compound metabolic process;hormone metabolic process;D-amino acid metabolic process;oxidation-reduction process
• Cellular component: peroxisome;peroxisomal matrix;cytosol
• Molecular function: D-amino-acid oxidase activity;signaling receptor binding;protein binding;D-aspartate oxidase activity;cofactor binding;FAD binding