GDA

guanine deaminase, the group of M38 metallopeptidases

Basic information

Region (hg38): 9:72114595-72257193

Links

ENSG00000119125

∙ NCBI:9615 ∙ OMIM:139260 ∙ HGNC:4212 ∙ Uniprot:Q9Y2T3 ∙ 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 GDA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GDA gene is commonly pathogenic or not. These statistics are base on transcript: . 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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			26 clinvar	3 clinvar		29
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	26	3	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GDA	protein_coding	protein_coding	ENST00000238018	15	142599

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.00133	125678	0	19	125697	0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	187	252	0.741	0.0000126	3083
Missense in Polyphen		44	95.5	0.46073		1122
Synonymous	-0.152	97	95.1	1.02	0.00000497	890
Loss of Function	4.56	2	28.1	0.0712	0.00000164	324

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000164	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000129	0.000123
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.000169	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Catalyzes the hydrolytic deamination of guanine, producing xanthine and ammonia. {ECO:0000250}.;
Pathway: Purine metabolism - Homo sapiens (human);Purine Nucleoside Phosphorylase Deficiency;Mercaptopurine Action Pathway;Azathioprine Action Pathway;Pyrimidine Metabolism;Xanthine Dehydrogenase Deficiency (Xanthinuria);Adenylosuccinate Lyase Deficiency;AICA-Ribosiduria;Thioguanine Action Pathway;Adenine phosphoribosyltransferase deficiency (APRT);Mitochondrial DNA depletion syndrome;Myoadenylate deaminase deficiency;Purine Metabolism;UMP Synthase Deiciency (Orotic Aciduria);MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy);Molybdenum Cofactor Deficiency;Adenosine Deaminase Deficiency;Gout or Kelley-Seegmiller Syndrome;Lesch-Nyhan Syndrome (LNS);Xanthinuria type I;Xanthinuria type II;Beta Ureidopropionase Deficiency;Dihydropyrimidinase Deficiency;Nucleobase catabolism;Metabolism of nucleotides;guanosine nucleotides degradation;purine nucleotides degradation;Metabolism;Purine nucleotides nucleosides metabolism;Purine catabolism (Consensus)

Recessive Scores

pRec: 0.282

Intolerance Scores

loftool: 0.128
rvis_EVS: 0.02
rvis_percentile_EVS: 55.45

Haploinsufficiency Scores

pHI: 0.446
hipred: Y
hipred_score: 0.765
ghis: 0.520

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.986

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Gda
Phenotype

Gene ontology

Biological process: nucleobase-containing compound metabolic process;guanine catabolic process;purine nucleotide catabolic process;nervous system development;guanine metabolic process
Cellular component: cytosol
Molecular function: zinc ion binding;guanine deaminase activity