ADAT2

adenosine deaminase tRNA specific 2, the group of Adenosine deaminases acting on RNA

Basic information

Region (hg38): 6:143422832-143450695

Previous symbols: [ "DEADC1" ]

Links

ENSG00000189007 ∙ NCBI:134637 ∙ OMIM:615388 ∙ HGNC:21172 ∙ Uniprot:Q7Z6V5 ∙ 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 ADAT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAT2 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			8			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	0	0

Variants in ADAT2

This is a list of pathogenic ClinVar variants found in the ADAT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-143428489-G-A		not specified	Uncertain significance (Nov 15, 2021)
6-143428491-A-C		not specified	Uncertain significance (Sep 01, 2021)
6-143428681-T-C		not specified	Uncertain significance (May 21, 2024)
6-143433948-G-C		not specified	Uncertain significance (Dec 07, 2021)
6-143433951-C-T		not specified	Uncertain significance (Apr 26, 2024)
6-143433961-C-G		not specified	Uncertain significance (Dec 06, 2021)
6-143438600-T-C			not provided (-)
6-143450587-C-G		not specified	Uncertain significance (Jul 10, 2023)
6-143450589-T-C		not specified	Uncertain significance (Dec 18, 2023)
6-143450634-G-T		not specified	Uncertain significance (Apr 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAT2	protein_coding	protein_coding	ENST00000237283	6	27842

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.01e-7	0.185	124759	0	38	124797	0.000152

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.880	87	113	0.767	0.00000598	1251
Missense in Polyphen		24	41.368	0.58016		472
Synonymous	0.295	38	40.4	0.941	0.00000213	359
Loss of Function	0.132	11	11.5	0.958	6.50e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000726	0.000726
Ashkenazi Jewish	0.00	0.00
East Asian	0.000111	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000124	0.000124
Middle Eastern	0.000111	0.000111
South Asian	0.000261	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably participates in deamination of adenosine-34 to inosine in many tRNAs. {ECO:0000250}.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.155

Intolerance Scores

• loftool: 0.618
• rvis_EVS: 0.19
• rvis_percentile_EVS: 66.82

Haploinsufficiency Scores

• pHI: 0.332
• hipred: N
• hipred_score: 0.213
• ghis: 0.530

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.378

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adat2

Gene ontology

• Biological process: tRNA wobble adenosine to inosine editing
• Cellular component: nucleoplasm;tRNA-specific adenosine-34 deaminase complex
• Molecular function: protein binding;zinc ion binding;tRNA-specific adenosine-34 deaminase activity