DTD1

D-aminoacyl-tRNA deacylase 1

Basic information

Region (hg38): 20:18587941-18766644

Previous symbols: [ "C20orf88", "HARS2" ]

Links

ENSG00000125821 ∙ NCBI:92675 ∙ OMIM:610996 ∙ HGNC:16219 ∙ Uniprot:Q8TEA8 ∙ 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 DTD1 gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DTD1 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in DTD1

This is a list of pathogenic ClinVar variants found in the DTD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-18588109-G-A		not specified	Uncertain significance (Aug 30, 2022)
20-18593777-G-T		not specified	Uncertain significance (Mar 08, 2024)
20-18596008-T-C		not specified	Uncertain significance (Aug 17, 2022)
20-18596029-G-C		not specified	Uncertain significance (May 08, 2023)
20-18596031-G-T		not specified	Uncertain significance (Jun 28, 2022)
20-18596149-T-G		not specified	Uncertain significance (May 17, 2023)
20-18596167-C-T		not specified	Uncertain significance (Feb 03, 2022)
20-18596185-T-C		not specified	Uncertain significance (Dec 17, 2023)
20-18596191-A-G		not specified	Uncertain significance (Aug 11, 2022)
20-18628153-G-A		not specified	Uncertain significance (Dec 20, 2023)
20-18628153-G-T		not specified	Uncertain significance (Sep 17, 2021)
20-18628159-A-G		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DTD1	protein_coding	protein_coding	ENST00000377452	5	176025

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00181	0.908	125742	0	6	125748	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	81	117	0.693	0.00000681	1364
Missense in Polyphen		27	41.786	0.64615		481
Synonymous	-0.112	48	47.0	1.02	0.00000299	402
Loss of Function	1.48	6	11.4	0.528	6.55e-7	131

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00	0.00
Finnish	0.0000468	0.0000462
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Possible ATPase (PubMed:15653697) involved in DNA replication, may facilitate loading of CDC45 onto pre-replication complexes (PubMed:20065034). {ECO:0000269|PubMed:15653697, ECO:0000269|PubMed:20065034}.

Recessive Scores

• pRec: 0.146

Intolerance Scores

• loftool: 0.189
• rvis_EVS: -0.21
• rvis_percentile_EVS: 38.28

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.329
• ghis: 0.616

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.165

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dtd1

Gene ontology

• Biological process: DNA replication;tRNA metabolic process;aminoacyl-tRNA metabolism involved in translational fidelity
• Cellular component: nucleolus;cytoplasm;cytosol
• Molecular function: tRNA binding;aminoacyl-tRNA editing activity;DNA binding;metal ion binding;D-tyrosyl-tRNA(Tyr) deacylase activity