GATB

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

Basic information

Region (hg38): 4:151670504-151761007

Previous symbols: [ "PET112L", "PET112" ]

Links

ENSG00000059691 ∙ NCBI:5188 ∙ OMIM:603645 ∙ HGNC:8849 ∙ Uniprot:O75879 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Combined oxidative phosphorylation deficiency 41	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; Neurologic	30283131

ClinVar

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

• Combined oxidative phosphorylation deficiency 41 (2 variants)
• Cardiomyopathy, mitochondrial (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GATB 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				4	4	8
missense	1		38	13	3	55
nonsense			1			1
start loss						0
frameshift	1		1			2
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1	1	4	6
non coding					14	14
Total	2	0	41	17	21

Highest pathogenic variant AF is 0.00000657

Variants in GATB

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

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

Position	Type	Phenotype	Significance	ClinVar
4-151671039-T-C			Benign (May 12, 2021)
4-151671194-C-T		not specified	Uncertain significance (Jan 10, 2022)
4-151671226-C-G		not specified	Uncertain significance (Nov 09, 2023)
4-151671226-C-T		not specified	Uncertain significance (Sep 25, 2023)
4-151671244-C-T		not specified	Uncertain significance (Jul 05, 2023)
4-151671245-G-A			Uncertain significance (Jan 01, 2024)
4-151671253-C-CCAAT		GATB-related disorder	Uncertain significance (Sep 07, 2022)
4-151671293-C-T		not specified	Uncertain significance (Apr 12, 2024)
4-151671304-TAGA-T		Combined oxidative phosphorylation deficiency 41	Uncertain significance (-)
4-151671317-A-ATTAC			Benign (May 12, 2021)
4-151672801-C-A		not specified	Uncertain significance (Jun 17, 2022)
4-151672828-T-A		not specified	Uncertain significance (Aug 16, 2021)
4-151679872-G-A		not specified	Uncertain significance (Jan 18, 2023)
4-151679994-T-G			Benign (May 12, 2021)
4-151688404-C-A			Benign (May 12, 2021)
4-151688542-A-G			Benign (May 12, 2021)
4-151688548-A-C			Benign (May 12, 2021)
4-151688632-C-T		GATB-related disorder	Benign (May 04, 2021)
4-151688674-A-C		GATB-related disorder	Benign (Nov 25, 2019)
4-151688768-TA-T		Combined oxidative phosphorylation deficiency 41 • GATB-related disorder	Benign (Sep 05, 2021)
4-151688768-TAA-T		GATB-related disorder	Benign (Nov 04, 2019)
4-151688768-T-TA		GATB-related disorder	Likely benign (Aug 01, 2023)
4-151688846-C-CA			Benign (May 12, 2021)
4-151688965-T-C			Benign (May 12, 2021)
4-151701339-A-G		GATB-related disorder	Uncertain significance (Mar 07, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GATB	protein_coding	protein_coding	ENST00000263985	13	90520

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.00e-10	0.784	125681	1	66	125748	0.000266

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.488	284	308	0.922	0.0000159	3631
Missense in Polyphen		116	133.07	0.87171		1566
Synonymous	-0.274	126	122	1.03	0.00000688	1100
Loss of Function	1.59	19	28.1	0.676	0.00000135	320

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000943	0.000941
Ashkenazi Jewish	0.00	0.00
East Asian	0.000110	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000205	0.000202
Middle Eastern	0.000110	0.000109
South Asian	0.000524	0.000523
Other	0.000525	0.000489

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_03147, ECO:0000269|PubMed:19805282}.
• Pathway: Aminoacyl-tRNA biosynthesis - Homo sapiens (human);L-glutamine tRNA biosynthesis (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• rvis_EVS: 0.36
• rvis_percentile_EVS: 74.66

Haploinsufficiency Scores

• pHI: 0.0528
• hipred: N
• hipred_score: 0.174
• ghis: 0.448

Essentials

• essential_gene_gene_trap: E

Mouse Genome Informatics

• Gene name: Gatb

Gene ontology

• Biological process: translation;mitochondrial translation;glutaminyl-tRNAGln biosynthesis via transamidation
• Cellular component: mitochondrion;glutamyl-tRNA(Gln) amidotransferase complex
• Molecular function: ATP binding;translation factor activity, RNA binding;glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity