TARS3

threonyl-tRNA synthetase 3

Basic information

Region (hg38): 15:101653596-101724473

Previous symbols: [ "TARSL2" ]

Links

ENSG00000185418 ∙ NCBI:123283 ∙ ∙ HGNC:24728 ∙ Uniprot:A2RTX5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TARS3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TARS3 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						0
missense			52	1		53
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	52	1	0

Variants in TARS3

This is a list of pathogenic ClinVar variants found in the TARS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-101654611-G-C		not specified	Uncertain significance (May 17, 2023)
15-101654641-T-C		not specified	Uncertain significance (May 16, 2023)
15-101654688-C-T		not specified	Uncertain significance (Jan 22, 2024)
15-101654727-A-G		not specified	Uncertain significance (Dec 18, 2023)
15-101656937-A-G		not specified	Uncertain significance (Feb 05, 2024)
15-101656955-T-A		not specified	Uncertain significance (Sep 20, 2023)
15-101656961-T-G		not specified	Uncertain significance (Jun 28, 2022)
15-101656976-T-C		not specified	Uncertain significance (Feb 28, 2024)
15-101657029-C-T		not specified	Uncertain significance (Jun 18, 2021)
15-101657030-T-C		not specified	Uncertain significance (Oct 27, 2022)
15-101657835-G-T		not specified	Uncertain significance (Sep 25, 2023)
15-101657837-C-T		not specified	Uncertain significance (Aug 02, 2022)
15-101661719-C-T		not specified	Uncertain significance (Mar 07, 2023)
15-101661773-C-T		not specified	Uncertain significance (Feb 26, 2024)
15-101661775-C-T		not specified	Uncertain significance (May 13, 2024)
15-101671548-A-C		not specified	Uncertain significance (Dec 14, 2023)
15-101675629-C-T		not specified	Uncertain significance (Nov 21, 2023)
15-101675667-T-C		not specified	Uncertain significance (Apr 08, 2024)
15-101684119-G-A		not specified	Uncertain significance (Nov 08, 2022)
15-101684160-T-C		not specified	Uncertain significance (Aug 08, 2022)
15-101684201-T-G		not specified	Uncertain significance (Jun 22, 2024)
15-101684218-G-A		not specified	Uncertain significance (Feb 27, 2023)
15-101684220-C-T		not specified	Uncertain significance (Nov 17, 2022)
15-101684228-A-T		not specified	Uncertain significance (Jul 13, 2021)
15-101685929-A-G		not specified	Uncertain significance (Feb 12, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TARS3	protein_coding	protein_coding	ENST00000335968	19	71007

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.74e-15	0.887	125621	0	127	125748	0.000505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.310	400	418	0.957	0.0000212	5302
Missense in Polyphen		104	119.12	0.87311		1491
Synonymous	-1.07	169	152	1.11	0.00000832	1415
Loss of Function	2.11	30	45.3	0.662	0.00000235	543

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000805	0.000803
Ashkenazi Jewish	0.00	0.00
East Asian	0.000763	0.000761
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000522	0.000519
Middle Eastern	0.000763	0.000761
South Asian	0.000824	0.000817
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Aminoacyl-tRNA biosynthesis - Homo sapiens (human);tRNA charging (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.304
• rvis_EVS: -1.53
• rvis_percentile_EVS: 3.37

Haploinsufficiency Scores

• pHI: 0.142
• hipred: N
• hipred_score: 0.384
• ghis: 0.637

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.116

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tarsl2

Gene ontology

• Biological process: threonyl-tRNA aminoacylation;biological_process
• Cellular component: cellular_component;nucleus;cytoplasm
• Molecular function: molecular_function;threonine-tRNA ligase activity;protein binding;ATP binding