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Intellectual disability - microarray and sequencing v3.1513 NUDT2 Arina Puzriakova Tag for-review was removed from gene: NUDT2.
Intellectual disability - microarray and sequencing v3.1510 NUDT2 Sarah Leigh commented on gene: NUDT2
Intellectual disability - microarray and sequencing v3.1509 NUDT2 Arina Puzriakova Source Expert Review Green was added to NUDT2.
Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
Intellectual disability - microarray and sequencing v3.510 NUDT2 Arina Puzriakova Classified gene: NUDT2 as Amber List (moderate evidence)
Intellectual disability - microarray and sequencing v3.510 NUDT2 Arina Puzriakova Added comment: Comment on list classification: This gene should be promoted to Green at the next GMS panel update (added 'for-review' tag). There are now at least 2 biallelic variants reported in 6 families - 3 of which present GDD and ID, while the remaining had delay but borderline intelligence.
Intellectual disability - microarray and sequencing v3.510 NUDT2 Arina Puzriakova Gene: nudt2 has been classified as Amber List (Moderate Evidence).
Intellectual disability - microarray and sequencing v3.509 NUDT2 Arina Puzriakova Tag founder-effect was removed from gene: NUDT2.
Tag for-review tag was added to gene: NUDT2.
Intellectual disability - microarray and sequencing v3.509 NUDT2 Arina Puzriakova Phenotypes for gene: NUDT2 were changed from Muscular hypotonia; Global developmental delay; Intellectual disability; no OMIM number to Muscular hypotonia; Global developmental delay; Intellectual disability; Polyneuropathy; no OMIM number
Intellectual disability - microarray and sequencing v3.508 NUDT2 Arina Puzriakova Publications for gene: NUDT2 were set to 27431290; 30059600
Intellectual disability - microarray and sequencing v3.507 NUDT2 Arina Puzriakova commented on gene: NUDT2
Intellectual disability - microarray and sequencing v3.500 NUDT2 Zornitza Stark reviewed gene: NUDT2: Rating: GREEN; Mode of pathogenicity: None; Publications: 27431290, 30059600, 33058507; Phenotypes: Muscular hypotonia, Global developmental delay, Intellectual disability, Polyneuropathy; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal; Current diagnostic: yes
Intellectual disability - microarray and sequencing v2.737 NUDT2 Ivone Leong Classified gene: NUDT2 as Amber List (moderate evidence)
Intellectual disability - microarray and sequencing v2.737 NUDT2 Ivone Leong Added comment: Comment on list classification: NUDT2 has been given an amber gene rating based on the evidence provided by Konstantinos Varvagiannis.
Intellectual disability - microarray and sequencing v2.737 NUDT2 Ivone Leong Gene: nudt2 has been classified as Amber List (Moderate Evidence).
Intellectual disability - microarray and sequencing v2.734 NUDT2 Ivone Leong Tag founder-effect tag was added to gene: NUDT2.
Intellectual disability - microarray and sequencing v2.734 NUDT2 Ivone Leong Phenotypes for gene: NUDT2 were changed from Muscular hypotonia; Global developmental delay; Intellectual disability to Muscular hypotonia; Global developmental delay; Intellectual disability; no OMIM number
Intellectual disability - microarray and sequencing v2.551 NUDT2 Konstantinos Varvagiannis gene: NUDT2 was added
gene: NUDT2 was added to Intellectual disability. Sources: Literature,Expert Review
Mode of inheritance for gene: NUDT2 was set to BIALLELIC, autosomal or pseudoautosomal
Publications for gene: NUDT2 were set to 27431290; 30059600
Phenotypes for gene: NUDT2 were set to Muscular hypotonia; Global developmental delay; Intellectual disability
Penetrance for gene: NUDT2 were set to Complete
Review for gene: NUDT2 was set to AMBER
Added comment: PMID: 27431290 reports briefly on 2 sibs from a consanguineous Saudi family, as part of a cohort of 337 patients investigated for intellectual disability. Both were homozygous for a nonsense NUDT2 mutation [NM_001161.4:c.34C>T or p.Arg12Ter / rs148119952]. The common features included hypotonia, global developmental delay (first words at 2.5 years, sitting at 2-2.5 years,walking achieved by 4 years - valid for both sibs) and intellectual disability. No other candidate variants were found in the exome.

PMID: 30059600 is a further report on 5 individuals from 3 consanguineous families from Saudi Arabia. All presented with low birth weight and height, poor suck, hypotonia, motor and language delay and borderline intelligence. All patients were homozygous for the same nonsense variant (Arg12Ter) which seems to be a founder mutation in Saudi Arabia.

As truncating NUDT2 variants have a combined allele frequency of 0.02% in gnomAD (no homozygotes in the database) the authors comment that most of the other LoF variants observed are in the second - and last - exon of the gene (thus probably escaping NMD) and downstream of its catalytic domain.

As a result this gene can be considered for inclusion in the ID panel probably as amber (single founder mutation - the degree of intellectual disability appears to be more severe in the first report but borderline in the subsequent) or green.
Sources: Literature, Expert Review