TARS1

threonyl-tRNA synthetase 1, the group of Aminoacyl tRNA synthetases, Class II

Basic information

Region (hg38): 5:33440696-33468091

Previous symbols: [ "TARS" ]

Links

ENSG00000113407 ∙ NCBI:6897 ∙ OMIM:187790 ∙ HGNC:11572 ∙ Uniprot:P26639 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• trichothiodystrophy (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Trichothiodystrophy 7, nonphotosensitive	AR	Allergy/Immunology/Infectious	The condition has been described as involve recurrent respiratory infections, and awareness may allow prompt diagnosis and management of infections	Allergy/Immunology/Infectious; Dermatologic; Musculoskeletal; Neurologic	31374204

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TARS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TARS1 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
missense			48	3	6	57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				5	2	7
non coding					3	3
Total	0	0	48	3	13

Variants in TARS1

This is a list of pathogenic ClinVar variants found in the TARS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-33441102-G-C		not specified	Uncertain significance (Apr 23, 2024)
5-33441112-C-T		not specified	Uncertain significance (Oct 04, 2022)
5-33441125-G-C		not specified	Uncertain significance (Jan 09, 2024)
5-33445328-G-A		Trichothiodystrophy 7, nonphotosensitive • TARS1-related disorder	Benign/Likely benign (May 17, 2022)
5-33445389-T-G		not specified	Uncertain significance (Mar 11, 2022)
5-33448548-C-T		not specified	Uncertain significance (Sep 20, 2023)
5-33448565-T-C		not specified	Uncertain significance (Jan 31, 2024)
5-33448599-C-T		TARS1-related disorder	Likely benign (May 22, 2023)
5-33448616-C-G		not specified	Uncertain significance (Jun 24, 2022)
5-33448633-A-C		TARS1-related disorder	Benign (Feb 08, 2018)
5-33448686-C-A		TARS1-related disorder	Benign (Jun 01, 2023)
5-33448701-C-T		not specified	Uncertain significance (Apr 25, 2022)
5-33452335-C-T		TARS1-related disorder	Benign (Nov 06, 2019)
5-33453263-CT-C		TARS1-related disorder	Likely benign (Oct 29, 2019)
5-33453263-CTT-C		TARS1-related disorder	Likely benign (Feb 20, 2020)
5-33453263-CTTT-C		TARS1-related disorder	Likely benign (Nov 12, 2019)
5-33453263-CTTTT-C		TARS1-related disorder	Likely benign (Nov 25, 2019)
5-33453263-C-CT		TARS1-related disorder	Likely benign (Nov 25, 2019)
5-33453311-G-A		TARS1-related disorder	Benign (Jan 30, 2018)
5-33453351-G-A		not specified	Uncertain significance (Jul 27, 2022)
5-33453366-A-G		not specified	Uncertain significance (Mar 20, 2024)
5-33455016-C-T		TARS1-related disorder	Benign (Feb 08, 2018)
5-33455042-A-G		not specified	Uncertain significance (Jun 02, 2024)
5-33455050-A-G		not specified	Uncertain significance (Mar 30, 2024)
5-33455059-G-A		not specified	Uncertain significance (Jan 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TARS1	protein_coding	protein_coding	ENST00000455217	20	28843

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.95e-13	0.994	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.15	354	420	0.842	0.0000224	5006
Missense in Polyphen		118	159.62	0.73927		1855
Synonymous	-0.316	148	143	1.03	0.00000756	1360
Loss of Function	2.67	27	46.7	0.578	0.00000251	540

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000964	0.000932
Ashkenazi Jewish	0.00	0.00
East Asian	0.000764	0.000761
Finnish	0.0000928	0.0000924
European (Non-Finnish)	0.000223	0.000220
Middle Eastern	0.000764	0.000761
South Asian	0.000171	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Aminoacyl-tRNA biosynthesis - Homo sapiens (human);tRNA Aminoacylation;Translation;Metabolism of proteins;Glycine Serine metabolism;tRNA charging;Cytosolic tRNA aminoacylation (Consensus)

Recessive Scores

• pRec: 0.144

Intolerance Scores

• loftool: 0.546
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.87

Haploinsufficiency Scores

• pHI: 0.838
• hipred: Y
• hipred_score: 0.648
• ghis: 0.589

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.957

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tars

Gene ontology

• Biological process: translation;tRNA aminoacylation for protein translation;threonyl-tRNA aminoacylation
• Cellular component: cytoplasm;cytosol;actin cytoskeleton;extracellular exosome
• Molecular function: tRNA binding;threonine-tRNA ligase activity;protein binding;ATP binding;protein homodimerization activity