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.

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	3		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	26	3	0

Variants in GDA

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

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

Position	Type	Phenotype	Significance	ClinVar
9-72195503-G-T		not specified	Uncertain significance (Nov 28, 2024)
9-72195561-C-T		not specified	Uncertain significance (Mar 21, 2023)
9-72195582-G-A		not specified	Uncertain significance (Oct 20, 2024)
9-72202639-G-A		not specified	Likely benign (May 07, 2024)
9-72210726-T-G		not specified	Uncertain significance (May 03, 2023)
9-72210759-C-T		not specified	Uncertain significance (Jan 24, 2024)
9-72213918-G-C		not specified	Uncertain significance (Sep 16, 2021)
9-72213940-C-T		not specified	Uncertain significance (Jul 27, 2024)
9-72223196-A-G		not specified	Likely benign (Jun 12, 2023)
9-72223198-A-T		not specified	Uncertain significance (Jun 07, 2024)
9-72223199-T-C		not specified	Uncertain significance (Dec 01, 2022)
9-72223210-C-T		not specified	Uncertain significance (Mar 11, 2022)
9-72225683-A-G		not specified	Likely benign (Dec 27, 2023)
9-72225744-A-G		not specified	Uncertain significance (Nov 01, 2022)
9-72225782-A-C		not specified	Uncertain significance (Nov 26, 2024)
9-72227987-C-A		not specified	Uncertain significance (Feb 01, 2023)
9-72228015-G-A		not specified	Uncertain significance (Jul 05, 2024)
9-72228028-A-G		not specified	Uncertain significance (Aug 22, 2023)
9-72231165-G-C		not specified	Uncertain significance (Mar 01, 2024)
9-72241154-G-C		not specified	Uncertain significance (Dec 21, 2022)
9-72241166-T-C		not specified	Uncertain significance (May 08, 2023)
9-72241167-A-G		not specified	Uncertain significance (Nov 19, 2022)
9-72245154-G-A		not specified	Uncertain significance (Aug 22, 2023)
9-72245160-A-G		not specified	Uncertain significance (Oct 22, 2024)
9-72245163-G-T		not specified	Uncertain significance (Aug 02, 2021)

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

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