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Genetic epilepsy syndromes

Gene: ADAT3

Amber List (moderate evidence)

ADAT3 (adenosine deaminase, tRNA specific 3)
EnsemblGeneIds (GRCh38): ENSG00000213638
EnsemblGeneIds (GRCh37): ENSG00000213638
OMIM: 615302, Gene2Phenotype
ADAT3 is in 2 panels

4 reviews

Rebecca Foulger (Genomics England curator)

I don't know

Review and rating collated by Tracy Lester (Oxford Medical Genetics Laboratories Oxford University Hospitals NHS Foundation Trust, 2019_02_06) on behalf of Wessex and West Midlands GLH for GMS Neurology specialist test group, for Clinical Indication R59 'Early onset or syndromic epilepsy'. Review contributors: Alison Callaway and John Taylor. Suggested gene rating: Amber.
Created: 6 Aug 2019, 8:38 p.m. | Last Modified: 6 Aug 2019, 8:38 p.m.
Panel Version: 1.189

Tracy Lester (Genetics laboratory, Oxford UK)

I don't know

PMID 26842963 mentions epilepsy, but limited evidence otherwise
Created: 6 Aug 2019, 8:31 p.m. | Last Modified: 6 Aug 2019, 8:31 p.m.
Panel Version: 1.188

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Mental retardation autosomal recessive 36, 615286

Publications

Sarah Leigh (Genomics England Curator)

Comment on list classification: Based one only two variants one of which is a founder
Created: 19 Oct 2018, 8:35 a.m.

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Initially reported in PMID 23620220, the findings in several individuals with biallelic ADAT3 pathogenic variants (including also those from the first report) are summarized in PMID 26842963.

A total of 39 individuals from 19 consanguineous families are described in the two studies. These individuals were homozygous for a specific missense variant (probably a Saudi Arabian founder mutation).

The common phenotype consists of intellectual disability (39/39 patients) and strabismus (32/39). Additional features included failure to thrive (33/39), microcephaly (22/39), short stature (11 of 15 individuals for whom this was information was available).

Epilepsy was observed in some of these individuals (6/39).

A few facial features were more common, although there was no distinct facial gestalt. //

PMID 30296593 reports on 2 additional subjects born to consanguineous parents and found to be homozygous for the same missense variant. These individuals presented with features similar to the previous reports (although none of them was reported to have seizures). //

Of note, the variant is either referred to as V144M (using NM_138422.2 or NM_138422.3) or as V128M (using NM_138422.1 as a reference / c.382G>A) as in the initial report. [ClinVar : https://www.ncbi.nlm.nih.gov/clinvar/variation/183301/#summary-evidence]

PMID 29796286 describes a 6-year-old female, born to consanguineous Iranian parents, investigated for developmental delay,intellectual disability, behavioral difficulties as well as microcephaly. A homozygous 8-basepair duplication in ADAT3 was identified by exome and was further confirmed by Sanger sequencing. This individual did not have seizures. //

This gene is included in DD/ID (but not epilepsy) panels offered by different diagnostic labs. //

As a result this gene can be considered for inclusion in the epilepsy panel as green (or amber).
Sources: Expert Review, Literature
Created: 16 Oct 2018, 12:48 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
# 615286. MENTAL RETARDATION, AUTOSOMAL RECESSIVE 36; MRT36

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Wessex and West Midlands GLH
  • NHS GMS
  • Expert Review Amber
Phenotypes
  • Mental retardation, autosomal recessive 36 615286
OMIM
615302
Clinvar variants
Variants in ADAT3
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

6 Aug 2019, Gel status: 2

Added New Source

Rebecca Foulger (Genomics England curator)

Source Wessex and West Midlands GLH was added to ADAT3.

6 Aug 2019, Gel status: 2

Added New Source

Rebecca Foulger (Genomics England curator)

Source NHS GMS was added to ADAT3.

11 Dec 2018, Gel status: 2

Panel promoted to version 1.0

Sarah Leigh (Genomics England Curator)

Konstantinos Varvagiannis: Initially reported in PMID 236

13 Nov 2018, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: adat3 has been classified as Amber List (Moderate Evidence).

13 Nov 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: ADAT3 were changed from # 615286. MENTAL RETARDATION, AUTOSOMAL RECESSIVE 36; MRT36 to Mental retardation, autosomal recessive 36 615286

19 Oct 2018, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: adat3 has been classified as Amber List (Moderate Evidence).

16 Oct 2018, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance

Konstantinos Varvagiannis (Other)

gene: ADAT3 was added gene: ADAT3 was added to Genetic Epilepsy Syndromes. Sources: Expert Review,Literature Mode of inheritance for gene: ADAT3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: ADAT3 were set to 23620220; 26842963; 30296593; 29796286 Phenotypes for gene: ADAT3 were set to # 615286. MENTAL RETARDATION, AUTOSOMAL RECESSIVE 36; MRT36 Penetrance for gene: ADAT3 were set to Complete Review for gene: ADAT3 was set to GREEN