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Undiagnosed metabolic disorders

Gene: PIGM

Amber List (moderate evidence)

PIGM (phosphatidylinositol glycan anchor biosynthesis class M)
EnsemblGeneIds (GRCh38): ENSG00000143315
EnsemblGeneIds (GRCh37): ENSG00000143315
OMIM: 610273, Gene2Phenotype
PIGM is in 5 panels

3 reviews

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with relevant phenotype in OMIM and as possible Gen2Phen gene. At least 1 variant was reported in 2 unrelated families (PMID 16767100), together with supportive functional studies (PMID 17442906 & 25293775).
Created: 19 Aug 2019, 3:43 p.m. | Last Modified: 19 Aug 2019, 3:43 p.m.
Panel Version: 1.237
Comment on phenotypes: Disorders of glycosphingolipid and glycosylphosphatidylinositol anchor glycosylation;Hypercoagulability syndrome due to glycosylphosphatidylinositol deficiency
Created: 19 Aug 2019, 3:22 p.m. | Last Modified: 19 Aug 2019, 3:22 p.m.
Panel Version: 1.235

Ellen McDonagh (Genomics England Curator)

Added tags to indicate a promoter variant has been reported.
Created: 1 Mar 2017, 11:54 a.m.

Olivia Niblock (Genomics England Curator)

Red List (low evidence)

Associated with phenotype in OMIM, not in G2P. At least 1 promoter variant reported in 3 cases from 2 unrelated consanguineous families. PIGM is subject to cell-type specific transcriptional regulation
Created: 23 Feb 2017, 5:15 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Glycosylphosphatidylinositol deficiency 610293

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Literature
Phenotypes
  • Glycosylphosphatidylinositol deficiency 610293
Tags
promoter curated-variant-list
OMIM
610273
Clinvar variants
Variants in PIGM
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

19 Aug 2019, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

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

19 Aug 2019, Gel status: 1

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: PIGM were set to 27604308; 25293775; 16767100

19 Aug 2019, Gel status: 1

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: PIGM were changed from Phosphatidylinositolglycan, class M deficiency (Disorders of glycosphingolipid and glycosylphosphatidylinositol anchor glycosylation); Glycosylphosphatidylinositol deficiency 610293 to Glycosylphosphatidylinositol deficiency 610293

1 Mar 2017, Gel status: 1

Set publications

Ellen McDonagh (Genomics England Curator)

Publications for PIGM were set to 27604308;25293775;16767100

27 Feb 2017, Gel status: 1

panel promoted to version 1

Sarah Leigh (Genomics England Curator)

Construction of “Undiagnosed Metabolic Disorders” (UDM) panel • The 614 genes from the neurometabolic gene panel (PMID: 27604308) added • Green genes downloaded from V1 metabolic panels (Cerebral folate deficiency, Congenital disorders of glycosylation, Hyperammonaemia, Ketotic hypoglycaemia, Mitochondrial disorders, Mucopolysaccharideosis, Gaucher, Fabry, Peroxisomal disorders), sources replaced with "Expert review green", then loaded as a review onto UDM panel, resulting in 367 green genes and 333 red (therefore 86 new green genes included from the additional metabolic panels that weren't previously on the UDM panel) • Downloaded green genes from all panels. Removed genes from none V1 panels. Removed genes from the metabolic panels mentioned above. Compared the remaining genes with the red genes from UDM panel. Loaded as an "Expert review Amber" review to the overlapping genes, (the panel name where the genes came from was used as the phenotype) • Used variant information from PMID 27604308 to review the genes on this panel • Reviewed genes on UDM panel with genes from Emory "Inherited Metabolic Disorders: Sequencing Panel" and UKGTN “Inborn Errors of Metabolism 226 panel”, changing status where appropriate, added 14 UKGTN genes that had not be listed before • Review 10 red genes that had not previously been reviewed, 4/10 were reclassified as green • Review the remaining 145 red genes that had not previously been reviewed (shared between reviewers EM, RF, LD, AT, HB, ON & SL), resulting in 60 green, 11 amber, 70 red, 4 I don’t know reviews) • Reviewed genes from PMID: 24816252 as a publication to genes found in the Inborn error or metabolism Genes metabolomics GWAS paper (figure 5). 2 new genes added

24 Feb 2017, Gel status: 1

Set Mode of Inheritance, Added New Source

Ellen McDonagh (Genomics England Curator)

PIGM was added to Undiagnosed metabolic disorderspanel. Source: Expert Review Red Model of inheritance for gene PIGM was set to BIALLELIC, autosomal or pseudoautosomal

28 Oct 2016, Gel status: 0

Created

Sarah Leigh (Genomics England Curator)

PIGM was created by sleigh

28 Oct 2016, Gel status: 0

Added New Source

Sarah Leigh (Genomics England Curator)

PIGM was added to Undiagnosed metabolic disorderspanel. Sources: Literature