Genes in panel

Inborn errors of metabolism

Gene: GALNT2

Amber List (moderate evidence)

GALNT2 (polypeptide N-acetylgalactosaminyltransferase 2)
EnsemblGeneIds (GRCh38): ENSG00000143641
EnsemblGeneIds (GRCh37): ENSG00000143641
OMIM: 602274, Gene2Phenotype
GALNT2 is in 6 panels

3 reviews

Arina Puzriakova (Genomics England Curator)

Comment on list classification: The rating of this gene should be reviewed at the date of next GMS panel update - there is sufficient evidence to rate this gene Green.
Created: 9 Oct 2020, 8:51 a.m. | Last Modified: 9 Oct 2020, 8:51 a.m.
Panel Version: 2.15

Sarah Leigh (Genomics England Curator)

Comment on list classification: Associated with relevant phenotype in OMIM, but not associated with phenotype in Gen2Phen. At least 5 variants reported in at least 5 unrelated cases, together with mouse and rat models (PMID 27508872;32293671).
Created: 23 Jun 2020, 11:03 a.m. | Last Modified: 9 Jul 2020, 1:48 p.m.
Panel Version: 2.14

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Seven individuals from four families reported with bi-allelic LOF variants and global developmental delay, intellectual disability with language deficit, autistic features, behavioural abnormalities, epilepsy, chronic insomnia, white matter changes on brain MRI, dysmorphic features, decreased stature, and decreased high density lipoprotein cholesterol levels. Rodent (mouse and rat) models of GALNT2-CDG recapitulated much of the human phenotype, including poor growth and neurodevelopmental abnormalities. Suggest adding to ID and epilepsy panels.
Sources: Literature
Created: 1 May 2020, 10:06 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Congenital disorder of glycosylation


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


Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
  • Literature
  • Expert Review Amber
  • Congenital disorder of glycosylation, type IIt 618885
Clinvar variants
Variants in GALNT2
Panels with this gene

History Filter Activity

5 Aug 2021, Gel status: 2

Removed Tag, Added Tag

Arina Puzriakova (Genomics England Curator)

Tag for-review was removed from gene: GALNT2. Tag Q2_21_rating tag was added to gene: GALNT2.

5 Aug 2021, Gel status: 2

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

Arina Puzriakova (Genomics England Curator)

gene: GALNT2 was added gene: GALNT2 was added to Inborn errors of metabolism. Sources: Expert Review Amber,Literature for-review tags were added to gene: GALNT2. Mode of inheritance for gene: GALNT2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: GALNT2 were set to 27508872; 32293671 Phenotypes for gene: GALNT2 were set to Congenital disorder of glycosylation, type IIt 618885