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Intellectual disability

Gene: PGM2L1

Green List (high evidence)
PGM2L1 (phosphoglucomutase 2 like 1)
EnsemblGeneIds (GRCh38): ENSG00000165434
EnsemblGeneIds (GRCh37): ENSG00000165434
OMIM: 611610, Gene2Phenotype
PGM2L1 is in 4 panels

3 reviews

Sarah Leigh (Genomics England Curator)

The rating of this gene has been updated following NHS Genomic Medicine Service approval.
Created: 14 Mar 2022, 2:22 p.m. | Last Modified: 14 Mar 2022, 2:22 p.m.
Panel Version: 3.1519
Created: 14 Mar 2022, 2:22 p.m.
Last Modified: 14 Mar 2022, 2:22 p.m.
Panel version: 3.1519

Arina Puzriakova (Genomics England Curator)

Comment on list classification: New gene added by Zornitza Stark. There is sufficient evidence to promote this gene to Green at the next GMS panel update (tagged).

Morava et al. 2021 (PMID: 33979636) identified 4 unrelated individuals with different biallelic protein-truncating variants in the PGM2L1 gene. All had severe GDD/ID. Other features that reach the threshold for inclusion on the relevant panels (observed in at least 3 cases) are epilepsy and early obesity (99th centile at ages 2 to 3). Some functional data included.
Created: 12 Aug 2021, 3:42 p.m. | Last Modified: 12 Aug 2021, 3:42 p.m.
Panel Version: 3.1218
Created: 12 Aug 2021, 3:42 p.m.
Last Modified: 12 Aug 2021, 3:42 p.m.
Panel version: 3.1218

Zornitza Stark (Australian Genomics)

Green List (high evidence)

PMID: 33979636:
- Bi-allelic PTVs in 4 unrelated individuals. All four affected individuals had severe developmental and speech delay, dysmorphic facial features, ear anomalies, high arched palate, strabismus, hypotonia, and keratosis pilaris. Early obesity and seizures were present in three individuals.
- Studies on patient fibroblasts and cell lines indicated that PGM2L1 deficiency causes a decrease, but not a disappearance, of the sugar bisphosphates needed for the formation of NDP-sugars and that there is no evidence that this leads to a glycosylation defect.
Sources: Literature
Created: 12 Jun 2021, 3:14 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Neurodevelopmental disorder

Publications

Created: 12 Jun 2021, 3:14 a.m.

Panel version: 3.1125

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
Phenotypes
  • Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191
OMIM
611610
Clinvar variants
Variants in PGM2L1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

7 Feb 2023, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: PGM2L1 were changed from Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191 to Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191

7 Feb 2023, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: PGM2L1 were changed from Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191 to Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191

7 Feb 2023, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: PGM2L1 were changed from Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191 to Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191

7 Feb 2023, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: PGM2L1 were changed from Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191 to Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191

7 Feb 2023, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: PGM2L1 were changed from Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191 to Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191

7 Feb 2023, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: PGM2L1 were changed from Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191 to Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191

7 Feb 2023, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: PGM2L1 were changed from Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191 to Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191

7 Feb 2023, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: PGM2L1 were changed from Neurodevelopmental disorder to Neurodevelopmental disorder with hypotonia, dysmorphic facies, and skin abnormalities, OMIM:620191

7 Feb 2023, Gel status: 3

Removed Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag gene-checked was removed from gene: PGM2L1.

10 May 2022, Gel status: 3

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag gene-checked tag was added to gene: PGM2L1.

14 Mar 2022, Gel status: 3

Removed Tag

Ivone Leong (Genomics England Curator)

Tag Q3_21_rating was removed from gene: PGM2L1.

14 Mar 2022, Gel status: 3

Added New Source, Status Update

Ivone Leong (Genomics England Curator)

Source Expert Review Green was added to PGM2L1. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

12 Aug 2021, Gel status: 2

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag Q3_21_rating tag was added to gene: PGM2L1.

12 Aug 2021, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: pgm2l1 has been classified as Amber List (Moderate Evidence).

12 Jun 2021, Gel status: 0

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

Zornitza Stark (Australian Genomics)

gene: PGM2L1 was added gene: PGM2L1 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: PGM2L1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PGM2L1 were set to 33979636 Phenotypes for gene: PGM2L1 were set to Neurodevelopmental disorder Review for gene: PGM2L1 was set to GREEN