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Intellectual disability

Gene: AGMO

Amber List (moderate evidence)

AGMO (alkylglycerol monooxygenase)
EnsemblGeneIds (GRCh38): ENSG00000187546
EnsemblGeneIds (GRCh37): ENSG00000187546
OMIM: 613738, Gene2Phenotype
AGMO is in 4 panels

2 reviews

Rebecca Foulger (Genomics England curator)

Comment on list classification: Gene was added to the panel and rated Green by Zornitza Stark. One family presented in PMID:27000257, and 2 compound het cases in PMID:31555905 (though there is one individual in gnomAD who is homozygous for the p.Gly144Arg variant). Functional data shows decreased enzyme activity of the variants. Although there are 3 cases, the phenotype is variable between patients (ID/DD vs regression) and therefore this is borderline. Therefore, rated as Amber awaiting further cases and clinical opinion.
Created: 1 Jun 2020, 8:01 p.m. | Last Modified: 1 Jun 2020, 8:02 p.m.
Panel Version: 3.78
PMID:31555905. Okur et al., report rare nonsense in-frame deletion and missense compound heterozygous variants in AGMO in 2 unrelated individuals (8 year old European girl, and 4-year old Ashkenazi Jewish boy). They demonstrated significantly diminished enzyme activity for all disease-associated variants. The girl harboured variants p.Trp130Ter & p.Gly238Cys. The boy harboured variants p.Gly144Arg and p.Tyr236del. Note that there is one individual in gnomAD who is homozygous for the p.Gly144Arg variant. Table 1 also mentions MTHFR C677T homozygous for the boy, but this is not referred to within the text. ID/DD (and seizures) were reported in the girl. The boy showed normal development to begin, but began to regress age 3.5 years.
Created: 1 Jun 2020, 4:48 p.m. | Last Modified: 1 Jun 2020, 7:54 p.m.
Panel Version: 3.77
PMID:27000257 (2016) Alrayes et al., 2016 enrolled a consanguineous family from Saudi Arabia presenting with primary microcephaly, developmental delay, short stature and intellectual disability. They identified a novel homozygous deletion mutation (c.967delA; p.Glu324Lysfs12*) in exon 10 of the alkylglycerol monooxygenase (AGMO) gene in 2 brothers. Population screening of 178 ethnically matched control chromosomes and consultation of the ExAC database confirmed that this variant was not present outside the family.
Created: 1 Jun 2020, 4:47 p.m. | Last Modified: 1 Jun 2020, 7:54 p.m.
Panel Version: 3.77

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Three unrelated families and functional data.
Sources: Expert list
Created: 27 Jan 2020, 5:48 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
microcephaly; intellectual disability; epilepsy

Publications

Variants in this GENE are reported as part of current diagnostic practice

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
Phenotypes
  • microcephaly
  • intellectual disability
  • epilepsy
  • developmental delay
OMIM
613738
Clinvar variants
Variants in AGMO
Penetrance
None
Publications
Panels with this gene

History Filter Activity

1 Jun 2020, Gel status: 2

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

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

1 Jun 2020, Gel status: 0

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: AGMO were changed from microcephaly; intellectual disability; epilepsy to microcephaly; intellectual disability; epilepsy; developmental delay

1 Jun 2020, Gel status: 0

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: AGMO were set to 31555905

27 Jan 2020, Gel status: 0

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

Zornitza Stark (Australian Genomics)

gene: AGMO was added gene: AGMO was added to Intellectual disability. Sources: Expert list Mode of inheritance for gene: AGMO was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: AGMO were set to 31555905 Phenotypes for gene: AGMO were set to microcephaly; intellectual disability; epilepsy Review for gene: AGMO was set to GREEN gene: AGMO was marked as current diagnostic