GATC

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

Basic information

Region (hg38): 12:120446443-120463749

Links

ENSG00000257218 ∙ NCBI:283459 ∙ OMIM:617210 ∙ HGNC:25068 ∙ Uniprot:O43716 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• combined oxidative phosphorylation deficiency 42 (Limited), mode of inheritance: Unknown

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 42	AR	General	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	Biochemical; Cardiovascular; Hematologic; Neurologic	30283131

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the GATC gene.

• not provided (8 variants)
• Inborn genetic diseases (5 variants)
• Combined oxidative phosphorylation deficiency 42 (2 variants)
• Cardiomyopathy, mitochondrial (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GATC 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				1	1	2
missense	1		5		1	7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2		4	6
Total	1	0	7	1	6

Variants in GATC

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

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

Position	Type	Phenotype	Significance	ClinVar
12-120446488-C-T			Benign (May 04, 2021)
12-120446525-C-T			Benign (May 04, 2021)
12-120446671-C-T			Likely benign (Jan 01, 2023)
12-120446698-G-T		not specified	Uncertain significance (Jun 29, 2023)
12-120446700-G-A		not specified	Uncertain significance (Dec 21, 2022)
12-120446703-T-C		Combined oxidative phosphorylation deficiency 42	Uncertain significance (Oct 19, 2022)
12-120446808-T-G		Cardiomyopathy, mitochondrial • Combined oxidative phosphorylation deficiency 42	Pathogenic (May 13, 2018)
12-120456882-C-T			Benign (May 12, 2021)
12-120457125-G-C		not specified	Uncertain significance (Jan 19, 2024)
12-120457131-C-G			Uncertain significance (Apr 25, 2017)
12-120457177-C-A		not specified	Uncertain significance (May 09, 2023)
12-120459756-C-T			Benign (May 12, 2021)
12-120459849-T-C			Benign (May 12, 2021)
12-120459969-T-G			Benign (May 04, 2021)
12-120462041-A-T		not specified	Uncertain significance (Jun 27, 2022)
12-120462080-C-T		not specified	Uncertain significance (Mar 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GATC	protein_coding	protein_coding	ENST00000551765	4	15149

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000659	0.518	125722	0	17	125739	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.223	77	82.7	0.931	0.00000406	859
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000312	0.000308
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000644	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

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}.
• Pathway: Aminoacyl-tRNA biosynthesis - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.105

Intolerance Scores

• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.229
• hipred: N
• hipred_score: 0.139
• ghis: 0.516

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.341

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gatc

Gene ontology

• Biological process: regulation of translational fidelity;mitochondrial translation;glutaminyl-tRNAGln biosynthesis via transamidation
• Cellular component: mitochondrion;glutamyl-tRNA(Gln) amidotransferase complex
• Molecular function: protein binding;ATP binding;glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity