DAO

D-amino acid oxidase

Basic information

Region (hg38): 12:108858932-108901043

Links

ENSG00000110887 ∙ NCBI:1610 ∙ OMIM:124050 ∙ HGNC:2671 ∙ Uniprot:P14920 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amyotrophic lateral sclerosis (Moderate), mode of inheritance: AD
• amyotrophic lateral sclerosis (Supportive), mode of inheritance: AD
• amyotrophic lateral sclerosis (Refuted Evidence), mode of inheritance: AD

ClinVar

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

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DAO 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				6	2	8
missense			29	3		32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1	1		2
non coding				1	16	17
Total	0	0	30	10	18

Variants in DAO

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

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

Position	Type	Phenotype	Significance	ClinVar
12-108884764-C-T			Benign (Jun 19, 2021)
12-108884971-T-G			Benign (Jun 18, 2021)
12-108885010-C-A		DAO-related disorder	Uncertain significance (May 16, 2023)
12-108885010-C-T		Inborn genetic diseases	Uncertain significance (Dec 04, 2023)
12-108885030-A-T		DAO-related disorder	Likely benign (Oct 03, 2022)
12-108885039-C-T		DAO-related disorder	Likely benign (Jan 07, 2019)
12-108885040-G-A		Amyotrophic lateral sclerosis	Uncertain significance (Jan 01, 2022)
12-108885051-C-T		DAO-related disorder	Likely benign (Dec 31, 2019)
12-108885052-G-A		Amyotrophic lateral sclerosis • DAO-related disorder	Conflicting classifications of pathogenicity (Feb 07, 2023)
12-108885067-G-A		Inborn genetic diseases	Uncertain significance (Nov 15, 2024)
12-108885107-T-A		Inborn genetic diseases	Uncertain significance (May 30, 2024)
12-108885114-G-A		DAO-related disorder	Likely benign (Mar 01, 2019)
12-108885118-C-T		DAO-related disorder	Uncertain significance (Dec 18, 2023)
12-108885119-G-A		DAO-related disorder	Uncertain significance (Mar 20, 2023)
12-108885138-C-A		DAO-related disorder	Likely benign (Nov 07, 2023)
12-108885153-C-T		DAO-related disorder	Likely benign (Dec 09, 2022)
12-108885154-GGCCTCT-G		DAO-related disorder	Likely benign (Jan 06, 2023)
12-108885166-C-A		Inborn genetic diseases	Uncertain significance (Oct 20, 2023)
12-108885179-A-T		Inborn genetic diseases	Uncertain significance (Jan 27, 2022)
12-108885193-C-G		DAO-related disorder	Likely benign (Aug 16, 2022)
12-108887351-C-T			Benign (Jun 19, 2021)
12-108887443-C-T		DAO-related disorder	Likely benign (Mar 23, 2023)
12-108887467-C-T		Amyotrophic lateral sclerosis	Uncertain significance (Mar 31, 2020)
12-108887476-A-G		Inborn genetic diseases	Uncertain significance (Jul 27, 2024)
12-108887505-G-A		Amyotrophic lateral sclerosis • DAO-related disorder	Uncertain significance (Dec 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DAO	protein_coding	protein_coding	ENST00000228476	10	42112

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.23e-22	0.000114	125594	0	153	125747	0.000609

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.108	196	200	0.979	0.0000122	2246
Missense in Polyphen		79	76.755	1.0292		829
Synonymous	0.393	74	78.4	0.944	0.00000476	694
Loss of Function	-1.13	29	23.1	1.25	0.00000131	228

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00165	0.00164
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000653	0.000653
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000352	0.000352
Middle Eastern	0.000653	0.000653
South Asian	0.00140	0.00141
Other	0.000978	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates the level of the neuromodulator D-serine in the brain. Has high activity towards D-DOPA and contributes to dopamine synthesis. Could act as a detoxifying agent which removes D-amino acids accumulated during aging. Acts on a variety of D- amino acids with a preference for those having small hydrophobic side chains followed by those bearing polar, aromatic, and basic groups. Does not act on acidic amino acids. {ECO:0000269|PubMed:17303072}.
• Disease: DISEASE: Schizophrenia (SCZD) [MIM:181500]: A complex, multifactorial psychotic disorder or group of disorders characterized by disturbances in the form and content of thought (e.g. delusions, hallucinations), in mood (e.g. inappropriate affect), in sense of self and relationship to the external world (e.g. loss of ego boundaries, withdrawal), and in behavior (e.g bizarre or apparently purposeless behavior). Although it affects emotions, it is distinguished from mood disorders in which such disturbances are primary. Similarly, there may be mild impairment of cognitive function, and it is distinguished from the dementias in which disturbed cognitive function is considered primary. Some patients manifest schizophrenic as well as bipolar disorder symptoms and are often given the diagnosis of schizoaffective disorder. {ECO:0000269|PubMed:12364586}. Note=Disease susceptibility may be associated with variations affecting the gene represented in this entry.
• Pathway: Arginine and proline metabolism - Homo sapiens (human);D-Arginine and D-ornithine metabolism - Homo sapiens (human);Peroxisome - Homo sapiens (human);Glycine, serine and threonine metabolism - Homo sapiens (human);D-Arginine and D-Ornithine Metabolism;Hyperornithinemia with gyrate atrophy (HOGA);Creatine deficiency, guanidinoacetate methyltransferase deficiency;L-arginine:glycine amidinotransferase deficiency;Hyperornithinemia-hyperammonemia-homocitrullinuria [HHH-syndrome];Guanidinoacetate Methyltransferase Deficiency (GAMT Deficiency);Prolinemia Type II;Prolidase Deficiency (PD);Arginine and Proline Metabolism;Hyperprolinemia Type I;Hyperprolinemia Type II;Ornithine Aminotransferase Deficiency (OAT Deficiency);Arginine: Glycine Amidinotransferase Deficiency (AGAT Deficiency);Metabolism of proteins;Metabolism of amino acids and derivatives;Glycine Serine metabolism;Metabolism;Peroxisomal protein import;Urea cycle and metabolism of arginine, proline, glutamate, aspartate and asparagine;Glyoxylate metabolism and glycine degradation;Glycine, serine, alanine and threonine metabolism (Consensus)

Recessive Scores

• pRec: 0.172

Intolerance Scores

• loftool: 0.561
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.16

Haploinsufficiency Scores

• pHI: 0.118
• hipred: N
• hipred_score: 0.216
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.732

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dao
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: proline catabolic process;protein targeting to peroxisome;cellular nitrogen compound metabolic process;D-serine catabolic process;dopamine biosynthetic process;D-amino acid metabolic process;oxidation-reduction process;D-alanine catabolic process;D-serine metabolic process
• Cellular component: mitochondrial outer membrane;peroxisome;peroxisomal membrane;peroxisomal matrix;cytosol
• Molecular function: D-amino-acid oxidase activity;signaling receptor binding;protein binding;protein dimerization activity;cofactor binding;FAD binding