GDA

protein-coding

guanine deaminase, the group of M38 metallopeptidases

Gene summary

This gene encodes an enzyme responsible for the hydrolytic deamination of guanine. Studies in rat ortholog suggest this gene plays a role in microtubule assembly. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

MANE transcript

NM_004293.5

Inheritance

—

ClinVar variants

U:52B:3

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.07

Max pathogenic AF

—

Genomic locus

chr9:72,114,595-72,257,193

External References & Databases

Ensembl (ENSG00000119125)

Transcript & Mutation Effects

hg38 • Region Span ~142.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GDA variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 46

not providedTotal: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004293.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			47 clinvar	3 clinvar		50
nonsense			1 clinvar			1
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	52	3	0	55

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004293.5	RefSeq	NP_004284.1	14	MANE Select
ENST00000358399.8	Ensembl	ENSP00000351170.4	14	MANE Select
NM_001242505.3	RefSeq	NP_001229434.1	15	Standard
NM_001242506.3	RefSeq	NP_001229435.1	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Purine metabolism - Homo sapiens (human)
Purine Nucleoside Phosphorylase Deficiency
Mercaptopurine Action Pathway
Azathioprine Action Pathway
Pyrimidine Metabolism

Biological Process

nucleobase-containing compound metabolic process
guanine catabolic process
purine nucleotide catabolic process
nervous system development
guanine metabolic process

Molecular Function

zinc ion binding
guanine deaminase activity

Cellular Component

cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000238018
Coding exons: 15
Length: 142599
Individuals with no LoFs: 125678
Homozygous LoFs: 0
Heterozygous LoFs: 19
Defined: 125697
p: 0.0000756

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.46	187	252	0.741	0.0000126	3083
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.000033	0.000033	rare
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Catalyzes the hydrolytic deamination of guanine, producing xanthine and ammonia. {ECO:0000250}.;

Recessive Scores

pRec: 0.282

Intolerance Scores

LoFtool: 0.128
RVIS EVS: 0.02
RVIS percentile EVS: 55.45

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.986

Gene Damage Prediction

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