ADAT3

Chr 19AR

adenosine deaminase tRNA specific 3

Also known as: FWP005, MRT36, MST121, MSTP121, NEDBGF, S863-5, TAD3

NCBI Gene: 113179 ENSG00000213638 UniProt: Q96EY9 OMIM: 615302

The protein functions as the regulatory subunit of a tRNA-specific adenosine deaminase complex that modifies tRNA anticodons to enable flexible genetic code reading and is required for proper neuronal migration during brain development. Mutations cause autosomal recessive neurodevelopmental disorder with brain abnormalities, poor growth, and dysmorphic facies, often presenting with intellectual disability and strabismus. The gene shows moderate tolerance to loss-of-function variants (LOEUF 1.459), consistent with recessive inheritance where heterozygous carriers are typically unaffected.

OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a subunit of a tRNA-specific adenosine deaminase. This heterodimeric enzyme converts adenosine to inosine in the tRNA anticodon. A mutation in this gene causes a syndrome characterized by intellectual disability and strabismus. This gene shares its 5' exon with the overlapping gene, secretory carrier membrane protein 4 (Gene ID: 113178). [provided by RefSeq, Jul 2016]

OMIM ResearchGenerating clinical summary…

ARLOEUF 1.461 OMIM phenotype

Clinical Summary— ADAT3

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Gene-Disease Validity (ClinGen)

intellectual disability-strabismus syndrome · ARModerate

Moderate evidence — consider for supplementary testing

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Population Constraint (gnomAD)

Low constraint (pLI 0.01) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

5 unique Pathogenic / Likely Pathogenic· 139 VUS of 178 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

1.46LOEUF

pLI 0.006

Z-score 0.80

OE 0.65 (0.32–1.46)

Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint?

-0.42Z-score

OE missense 1.08 (0.97–1.20)

235 obs / 217.5 exp

Tolerant

Tolerant to missense variation

Observed / Expected Ratios?

LoF OE?0.65 (0.32–1.46)

0≤0.351.4

Missense OE?1.08 (0.97–1.20)

0≤0.61.4

Synonymous OE?0.97

0≤1.21.6

LoF obs/exp: 4 / 6.1Missense obs/exp: 235 / 217.5Syn Z: 0.21

ClinVar Variant Classifications

178 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic1

Likely Pathogenic4

VUS139

Likely Benign23

Benign5

Conflicting6

Pathogenic

Likely Pathogenic

139

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	1	0	0	0	1
Likely Pathogenic	2	2	0	0	4
VUS	3	136	0	0	139
Likely Benign	0	6	0	17	23
Benign	0	1	0	4	5
Conflicting	—				6
Total	6	145	0	21	178

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

24 pathogenic / likely-pathogenic (of 37) ClinVar copy-number / structural variants overlap ADAT3 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →