GATC

protein-coding

glutamyl-tRNA amidotransferase subunit C, the group of Glutamyl-tRNA amidotransferase subunits

Gene summary

Predicted to enable ATP binding activity and glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity. Involved in glutaminyl-tRNAGln biosynthesis via transamidation and mitochondrial translation. Located in mitochondrion. Part of glutamyl-tRNA(Gln) amidotransferase complex. Implicated in combined oxidative phosphorylation deficiency 42. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_176818.3

Inheritance

ClinVar variants

P:1U:18B:9

Top phenotype

Combined oxidative phosphorylation deficiency 42

gnomAD constraint

pLI —, LoF o/e 0.87

Max pathogenic AF

—

Genomic locus

chr12:120,446,444-120,463,749

External References & Databases

Ensembl (ENSG00000257218)

Transcript & Mutation Effects

hg38 • Region Span ~17.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

combined oxidative phosphorylation deficiency 42LIMITED

Inheritance Pattern: Unknown

Disease ID:MONDO:0030008

Submitter: Labcorp Genetics (formerly Invitae)

inborn mitochondrial metabolism disorderLIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0004069

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Combined oxidative phosphorylation deficiency 42AR

Manifestation: Biochemical; Cardiovascular; Hematologic; Neurologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 30283131

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to GATC variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 21

not providedTotal: 6

Combined oxidative phosphorylation deficiency 42Total: 3

Cardiomyopathy, mitochondrialTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_176818.3. 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				8 clinvar		8
missense	1 clinvar		16 clinvar	1 clinvar		18
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	1	0	18	9	0	28

Highest pathogenic variant AF is 0.0000013693266

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 8 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_176818.3	RefSeq	NP_789788.1	4	MANE Select
ENST00000551765.6	Ensembl	ENSP00000446872.1	4	MANE Select
ENST00000229384.5	Ensembl	ENSP00000229384.5	3	Standard
ENST00000548171.1	Ensembl	ENSP00000448397.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Aminoacyl-tRNA biosynthesis - Homo sapiens (human)

Biological Process

regulation of translational fidelity
mitochondrial translation
glutaminyl-tRNAGln biosynthesis via transamidation

Molecular Function

protein binding
ATP binding
glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity

Cellular Component

mitochondrion
glutamyl-tRNA(Gln) amidotransferase complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000551765
Coding exons: 4
Length: 15149
Individuals with no LoFs: 125722
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125739
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.223	77	82.7	0.931	0.00000406	859
Missense (PolyPhen)		19	18.118	1.0487		211
Synonymous	0.272	35	37.1	0.943	0.00000193	289
Loss of Function	0.298	5	5.77	0.866	2.46e-7	66

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000064	0.000062	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Allows the formation of correctly charged Gln-tRNA(Gln) through the transamidation of misacylated Glu-tRNA(Gln) in the mitochondria. The reaction takes place in the presence of glutamine and ATP through an activated gamma-phospho-Glu- tRNA(Gln). {ECO:0000255|HAMAP-Rule:MF_03149, ECO:0000269|PubMed:19805282}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

RVIS EVS: -0.1
RVIS percentile EVS: 46.49

Essentials

Essential (CRISPR): N
Essential (CRISPR2): S
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.341

Gene Damage Prediction

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