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Undiagnosed metabolic disorders

Gene: SLC6A20

Red List (low evidence)
SLC6A20 (solute carrier family 6 member 20)
EnsemblGeneIds (GRCh38): ENSG00000163817
EnsemblGeneIds (GRCh37): ENSG00000163817
OMIM: 605616, Gene2Phenotype
SLC6A20 is in 5 panels

1 review

Sarah Leigh (Genomics England Curator)

Red List (low evidence)

The gene disease associations of SLC6A20 with Hyperglycinuria (OMIM:138500) and Iminoglycinuria, digenic (OMIM:242600) have been refuted in OMIM. The single SLC6A20 variant rs17279437 has been reclassified as a polymorphism, because it is present in 19,986 of 278,932 alleles and in 856 homozygotes in the gnomAD database (v2.1.1), for an allele frequency of 0.07165 (Personal Communication to OMIM from Hamosh, A. Baltimore, Md. 3rd April 2023).
Created: 17 Oct 2023, 9:50 a.m. | Last Modified: 17 Oct 2023, 9:50 a.m.
Panel Version: 1.600
Associated with phenotype in OMIM, not in G2P. One variant reported in 5 families, Hyperglycinuria 138500 results from heterozygous variant and Iminoglycinuria, digenic 242600 from homozygous variants
Created: 27 Feb 2017, 12:44 p.m.

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Phenotypes
Hyperglycinuria 138500; Iminoglycinuria, digenic 242600

Publications

Created: 27 Feb 2017, 12:44 p.m.

Panel version: 1.600

Details

Mode of Inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert Review Red
  • UKGTN
  • Literature
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Hyperglycinuria 138500
  • Iminoglycinuria, digenic 242600
Tags
refuted
OMIM
605616
Clinvar variants
Variants in SLC6A20
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

17 Oct 2023, Gel status: 1

Added Tag

Sarah Leigh (Genomics England Curator)

Tag refuted tag was added to gene: SLC6A20.

17 Oct 2023, Gel status: 1

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: slc6a20 has been classified as Red List (Low Evidence).

27 Feb 2017, Gel status: 3

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

27 Feb 2017, Gel status: 3

Upload gene information

Sarah Leigh (Genomics England Curator)

SLC6A20 was added to Undiagnosed metabolic disorderspanel. Sources: UKGTN

27 Feb 2017, Gel status: 2

Added New Source

Sarah Leigh (Genomics England Curator)

SLC6A20 was added to Undiagnosed metabolic disorderspanel. Sources: Radboud University Medical Center, Nijmegen,Literature,Illumina TruGenome Clinical Sequencing Services

27 Feb 2017, Gel status: 0

Created

Sarah Leigh (Genomics England Curator)

SLC6A20 was created by sleigh