ADAT3

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

Basic information

Region (hg38): 19:1905399-1913447

Links

ENSG00000213638NCBI:113179OMIM:615302HGNC:25151Uniprot:Q96EY9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Neurodevelopmental disorder with brain abnormalities, poor growth, and dysmorphic faciesARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Musculoskeletal; Neurologic23620220; 26842963; 29796286; 30296593

ClinVar

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

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
11
clinvar
6
clinvar
17
missense
1
clinvar
71
clinvar
4
clinvar
1
clinvar
77
nonsense
0
start loss
0
frameshift
1
clinvar
2
clinvar
3
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 2 75 15 7

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)498817
19-1912069-TGTCTCCCACAGTCG-T Likely pathogenic (Nov 03, 2020)1331555
19-1912083-G-A Likely benign (Feb 28, 2018)771509
19-1912101-G-C Intellectual disability-strabismus syndrome Uncertain significance (Aug 08, 2019)1029127
19-1912103-C-T Inborn genetic diseases Uncertain significance (Apr 12, 2023)2519848
19-1912105-G-A Inborn genetic diseases Uncertain significance (Apr 24, 2024)3268963
19-1912106-C-T not specified • Intellectual disability-strabismus syndrome Uncertain significance (Oct 05, 2018)434081
19-1912109-C-G not specified Uncertain significance (Jan 18, 2017)434082
19-1912114-C-T not specified Uncertain significance (Dec 29, 2017)1336464
19-1912125-G-T Inborn genetic diseases Uncertain significance (Jan 07, 2022)2270733
19-1912134-C-G Inborn genetic diseases Uncertain significance (Aug 02, 2023)2615617
19-1912141-G-GCCGGGAGC Intellectual disability-strabismus syndrome Pathogenic (Sep 10, 2021)549839
19-1912155-G-C Inborn genetic diseases Uncertain significance (Nov 09, 2022)2502139
19-1912158-T-G Likely benign (Apr 01, 2023)726301
19-1912163-C-T Inborn genetic diseases Uncertain significance (Jun 18, 2021)2233181
19-1912164-G-A Benign/Likely benign (Jun 01, 2024)718244
19-1912165-G-T Inborn genetic diseases Uncertain significance (Sep 29, 2023)3080681
19-1912194-C-T Likely benign (Jan 01, 2024)3025735
19-1912198-A-C Inborn genetic diseases Likely benign (Feb 17, 2022)2277878
19-1912205-CAG-C Intellectual disability-strabismus syndrome Likely pathogenic (Sep 22, 2024)3362604
19-1912208-G-A Inborn genetic diseases Uncertain significance (Aug 02, 2023)2596524
19-1912228-G-T Inborn genetic diseases Conflicting classifications of pathogenicity (Jan 01, 2024)2346490
19-1912252-A-C Inborn genetic diseases Uncertain significance (Jun 17, 2024)3268973
19-1912262-C-T Inborn genetic diseases Uncertain significance (Nov 03, 2022)2322263
19-1912263-C-G Benign/Likely benign (Aug 01, 2024)788009

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
ADAT3protein_codingprotein_codingENST00000329478 18068
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.005610.7361209570231209800.0000951
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.4222352171.080.00001712220
Missense in Polyphen4847.5181.0101507
Synonymous0.2141031060.9740.00000912822
Loss of Function0.80346.150.6512.66e-776

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00002970.0000297
Ashkenazi Jewish0.000.00
East Asian0.00005760.0000563
Finnish0.0002170.000148
European (Non-Finnish)0.0001260.000121
Middle Eastern0.00005760.0000563
South Asian0.0001660.000164
Other0.000.00

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
essential_gene_gene_trap
gene_indispensability_pred
E
gene_indispensability_score
0.854

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Adat3
Phenotype

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