ADAT1

adenosine deaminase tRNA specific 1, the group of Adenosine deaminases acting on RNA

Basic information

Region (hg38): 16:75596868-75623300

Links

ENSG00000065457 ∙ NCBI:23536 ∙ OMIM:604230 ∙ HGNC:228 ∙ Uniprot:Q9BUB4 ∙ 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 ADAT1 gene.

• not_specified (76 variants)
• not_provided (2 variants)
• Prostate_cancer (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001324445.2. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			73	4		77
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	73	6	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAT1	protein_coding	protein_coding	ENST00000307921	9	26320

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.54e-13	0.130	125644	0	103	125747	0.000410

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.47	343	275	1.25	0.0000142	3278
Missense in Polyphen		144	122.9	1.1717		1450
Synonymous	-1.41	122	104	1.18	0.00000595	972
Loss of Function	0.805	22	26.5	0.831	0.00000147	293

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00148	0.00148
Ashkenazi Jewish	0.00	0.00
East Asian	0.000598	0.000598
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000423	0.000422
Middle Eastern	0.000598	0.000598
South Asian	0.000327	0.000327
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Specifically deaminates adenosine-37 to inosine in tRNA- Ala.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.101

Intolerance Scores

• loftool: 0.295
• rvis_EVS: 0.8
• rvis_percentile_EVS: 87.66

Haploinsufficiency Scores

• pHI: 0.131
• hipred: N
• hipred_score: 0.177
• ghis: 0.491

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.916

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adat1

Gene ontology

• Biological process: tRNA processing
• Molecular function: RNA binding;tRNA-specific adenosine deaminase activity;metal ion binding