GATD1

protein-coding

glutamine amidotransferase class 1 domain containing 1, the group of Glutamine amidotransferase class 1 domain containing

Gene summary

Predicted to enable glyoxalase III activity. Predicted to be involved in obsolete methylglyoxal catabolic process to pyruvate via (R)-S-lactoyl-glutathione. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

PDDC1

MANE transcript

NM_182612.4

Inheritance

—

ClinVar variants

U:55B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.2

Max pathogenic AF

—

Genomic locus

chr11:767,220-777,488

External References & Databases

Ensembl (ENSG00000177225)

Transcript & Mutation Effects

hg38 • Region Span ~10.3 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 GATD1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 52

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182612.4. 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			53 clinvar	1 clinvar		54
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	55	1	0	56

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 34 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182612.4	RefSeq	NP_872418.1	8	MANE Select
ENST00000319863.13	Ensembl	ENSP00000321691.8	8	MANE Select
NM_001318818.2	RefSeq	NP_001305747.1	6	Standard
NM_001318820.2	RefSeq	NP_001305749.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

molecular_function

Cellular Component

extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000319863
Coding exons: 8
Length: 10269
Individuals with no LoFs: 125616
Homozygous LoFs: 0
Heterozygous LoFs: 50
Defined: 125666
p: 0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.389	125	138	0.907	0.00000935	1414
Missense (PolyPhen)		31	39.002	0.79484		337
Synonymous	-1.03	74	63.6	1.16	0.00000496	441
Loss of Function	2.34	2	9.97	0.201	4.24e-7	123

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00044	0.00044	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00030	0.00028	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.6
RVIS percentile EVS: 17.91

Essentials

Essential (gene trap): N