ADAT3

adenosine deaminase tRNA specific 3, the group of Adenosine deaminases acting on RNA

Basic information

Region (hg38): 19:1905398-1913447

Links

ENSG00000213638 ∙ NCBI:113179 ∙ OMIM:615302 ∙ HGNC:25151 ∙ Uniprot:Q96EY9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability-strabismus syndrome (Moderate), mode of inheritance: AR
• intellectual disability-strabismus syndrome (Supportive), mode of inheritance: AR
• intellectual disability-strabismus syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with brain abnormalities, poor growth, and dysmorphic facies	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	23620220; 26842963; 29796286; 30296593

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ADAT3 gene.

• not provided (33 variants)
• Inborn genetic diseases (28 variants)
• Intellectual disability-strabismus syndrome (22 variants)
• not specified (17 variants)
• Intellectual disability (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ADAT3 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				9	6	15
missense		1	57	5	1	64
nonsense						0
start loss						0
frameshift		1	2			3
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	2	60	14	7

Highest pathogenic variant AF is 0.0000920

Variants in ADAT3

This is a list of pathogenic ClinVar variants found in the ADAT3 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-1912063-C-T			Uncertain significance (Nov 30, 2016)
19-1912069-TGTCTCCCACAGTCG-T			Likely pathogenic (Nov 03, 2020)
19-1912083-G-A			Likely benign (Feb 28, 2018)
19-1912101-G-C		Intellectual disability-strabismus syndrome	Uncertain significance (Aug 08, 2019)
19-1912103-C-T		Inborn genetic diseases	Uncertain significance (Apr 12, 2023)
19-1912106-C-T		not specified • Intellectual disability-strabismus syndrome	Uncertain significance (Oct 05, 2018)
19-1912109-C-G		not specified	Uncertain significance (Jan 18, 2017)
19-1912114-C-T		not specified	Uncertain significance (Dec 29, 2017)
19-1912125-G-T		Inborn genetic diseases	Uncertain significance (Jan 07, 2022)
19-1912134-C-G		Inborn genetic diseases	Uncertain significance (Aug 02, 2023)
19-1912141-G-GCCGGGAGC		Intellectual disability-strabismus syndrome	Pathogenic (Sep 10, 2021)
19-1912155-G-C		Inborn genetic diseases	Uncertain significance (Nov 09, 2022)
19-1912158-T-G			Likely benign (Apr 01, 2023)
19-1912163-C-T		Inborn genetic diseases	Uncertain significance (Jun 18, 2021)
19-1912164-G-A			Benign/Likely benign (Apr 01, 2024)
19-1912165-G-T		Inborn genetic diseases	Uncertain significance (Sep 29, 2023)
19-1912194-C-T			Likely benign (Jan 01, 2024)
19-1912198-A-C		Inborn genetic diseases	Likely benign (Feb 17, 2022)
19-1912208-G-A		Inborn genetic diseases	Uncertain significance (Aug 02, 2023)
19-1912228-G-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Jan 01, 2024)
19-1912262-C-T		Inborn genetic diseases	Uncertain significance (Nov 03, 2022)
19-1912263-C-G			Benign (Dec 31, 2019)
19-1912298-C-G		Inborn genetic diseases	Uncertain significance (Sep 16, 2021)
19-1912305-C-T			Likely benign (Dec 31, 2019)
19-1912321-A-C			Uncertain significance (Apr 14, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ADAT3	protein_coding	protein_coding	ENST00000329478	1	8068

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00561	0.736	120957	0	23	120980	0.0000951

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.422	235	217	1.08	0.0000171	2220
Missense in Polyphen		48	47.518	1.0101		507
Synonymous	0.214	103	106	0.974	0.00000912	822
Loss of Function	0.803	4	6.15	0.651	2.66e-7	76

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000297	0.0000297
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000576	0.0000563
Finnish	0.000217	0.000148
European (Non-Finnish)	0.000126	0.000121
Middle Eastern	0.0000576	0.0000563
South Asian	0.000166	0.000164
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Disease: DISEASE: Mental retardation, autosomal recessive 36 (MRT36) [MIM:615286]: A disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. MRT36 is often associated with esotropia and failure to thrive. Other more variable features included microcephaly, hypotonia, and mild brain abnormalities on MRI, such as dilated ventricles or delayed myelination. {ECO:0000269|PubMed:23620220}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Recessive Scores

• pRec: 0.116

Haploinsufficiency Scores

• pHI: 0.225
• hipred: N
• hipred_score: 0.383
• ghis: 0.568

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.854

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Adat3

Gene ontology

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