DTD2

D-aminoacyl-tRNA deacylase 2

Basic information

Region (hg38): 14:31446036-31457506

Previous symbols: [ "C14orf126" ]

Links

ENSG00000129480 ∙ NCBI:112487 ∙ ∙ HGNC:20277 ∙ Uniprot:Q96FN9 ∙ 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 DTD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DTD2 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in DTD2

This is a list of pathogenic ClinVar variants found in the DTD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-31448191-C-T		not specified	Uncertain significance (Dec 22, 2023)
14-31448193-T-C		not specified	Uncertain significance (Dec 02, 2022)
14-31457357-G-A		not specified	Uncertain significance (May 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DTD2	protein_coding	protein_coding	ENST00000310850	3	11475

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000759	0.548	125717	1	30	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.760	67	86.9	0.771	0.00000439	1073
Missense in Polyphen		24	31.957	0.75101		391
Synonymous	-0.0157	34	33.9	1.00	0.00000180	332
Loss of Function	0.378	5	6.00	0.833	2.51e-7	83

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000450	0.000397
East Asian	0.000163	0.000163
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000620	0.0000615
Middle Eastern	0.000163	0.000163
South Asian	0.000547	0.000490
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Deacylates mischarged D-aminoacyl-tRNAs (By similarity). Probably acts by rejecting L-amino acids from its binding site rather than specific recognition of D-amino acids (By similarity). Catalyzes the hydrolysis of D-tyrosyl-tRNA(Tyr), has no activity on correctly charged L-tyrosyl-tRNA(Tyr) (By similarity). By recycling D-aminoacyl-tRNA to D-amino acids and free tRNA molecules, this enzyme counteracts the toxicity associated with the formation of D-aminoacyl-tRNA entities in vivo and helps enforce protein L-homochirality. In contrast to DTD1, deacylates L-Ala mischarged on tRNA(Thr)(G4.U69) by alanine-tRNA ligase AARS (PubMed:29410408). Can deacylate L-Ala due to a relaxed specificity for substrate chirality caused by the trans conformation of the Gly-Pro motif in the active site (PubMed:29410408). Also hydrolyzes correctly charged, achiral, glycyl-tRNA(Gly) in vitro, although in vivo EEF1A1/EF-Tu may protect cognate achiral glycyl-tRNA(Gly) from DTD2-mediated deacetylation (By similarity). {ECO:0000250|UniProtKB:Q8BHA3, ECO:0000269|PubMed:29410408}.

Recessive Scores

• pRec: 0.0710

Intolerance Scores

• rvis_EVS: -0.05
• rvis_percentile_EVS: 49.39

Haploinsufficiency Scores

• pHI: 0.260
• hipred: N
• hipred_score: 0.112
• ghis: 0.591

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dtd2

Gene ontology

• Biological process: tRNA metabolic process;aminoacyl-tRNA metabolism involved in translational fidelity
• Cellular component: cytoplasm
• Molecular function: tRNA binding;aminoacyl-tRNA editing activity;protein binding;D-tyrosyl-tRNA(Tyr) deacylase activity;Ala-tRNA(Thr) hydrolase activity