1. Panels
  2. Likely inborn error of metabolism
  3. SLC6A19
Genes in panel
Prev Next

Likely inborn error of metabolism

Gene: SLC6A19

Green List (high evidence)
SLC6A19 (solute carrier family 6 member 19)
EnsemblGeneIds (GRCh38): ENSG00000174358
EnsemblGeneIds (GRCh37): ENSG00000174358
OMIM: 608893, Gene2Phenotype
SLC6A19 is in 7 panels

3 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

The mode of inheritance of this gene has been updated to BIALLELIC, autosomal or pseudoautosomal following NHS Genomic Medicine Service approval.
Created: 26 Sep 2024, 3:37 p.m. | Last Modified: 26 Sep 2024, 3:37 p.m.
Panel Version: 6.10
Comment on mode of inheritance: As reviewed by Tracy Lester, SLC6A19 is associated with Hartnup disorder (MIM #234500), which is caused by biallelic variants. SLC6A19 is currently associated with Hyperglycinuria (MIM #138500) and Iminoglycinuria (MIM #242600) in both PanelApp and PanelApp Australia and hence the MOI was set to both monoallelic and biallelic. However, these phenotypes are caused by SLC36A2.

The association in PanelApp was due to the speculation in PMID:19033659 that combination of variants in SLC36A2 with variants in SLC6A20 or SLC6A19 may have contributed to these phenotypes in three of the reported families. The identified variant from SLC6A19 has now been classified as polymorphism because it was present in 62,195 of 282,492 alleles and in 7,227 homozygotes in the gnomAD database (v2.1.1), for an allele frequency of 0.2202 (https://www.omim.org/entry/608893?search=slc6a19&highlight=slc6a19#allelicVariants)nts)

Hence, the MOI should be updated to 'BIALLELIC, autosomal or pseudoautosomal' in the next GMS update.
Created: 11 Jun 2024, 5:10 p.m. | Last Modified: 11 Jun 2024, 5:10 p.m.
Panel Version: 5.5

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Hartnup disorder, OMIM:234500

Created: 11 Jun 2024, 5:07 p.m.
Last Modified: 11 Jun 2024, 5:07 p.m.
Panel version: 6.10

Tracy Lester (Genetics laboratory, Oxford UK)

Green List (high evidence)

I am not sure why this gene has been added with monoallelic inheritance as an option as Hartnup is a recessive condition. Suggest inheritance is changed to biallelic only
Created: 20 Feb 2024, 10:13 a.m. | Last Modified: 20 Feb 2024, 10:13 a.m.
Panel Version: 4.129

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

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

Created: 20 Feb 2024, 10:13 a.m.
Last Modified: 20 Feb 2024, 10:13 a.m.
Panel version: 4.129

Sarah Leigh (Genomics England Curator)

Comment when marking as ready: Associated with phenotypes in OMIM, not in G2P / DD. At least 6 variants reported in 8 cases of Hartnup disorder 234500
Created: 19 Jan 2017, 11:16 a.m.
Created: 19 Jan 2017, 11:16 a.m.

Panel version: Imported from Undiagnosed metabolic disorders panel version 0.227

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • London North GLH
  • NHS GMS
  • Expert Review Green
Phenotypes
  • Hartnup disorder, OMIM:234500
OMIM
608893
Clinvar variants
Variants in SLC6A19
Penetrance
None
Publications
Panels with this gene

History Filter Activity

26 Sep 2024, Gel status: 3

Removed Tag, Removed Tag, Removed Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q2_24_MOI was removed from gene: SLC6A19. Tag Q2_24_expert_review was removed from gene: SLC6A19. Tag Q2_24_NHS_review was removed from gene: SLC6A19.

26 Sep 2024, Gel status: 3

Set mode of inheritance

Achchuthan Shanmugasundram (Genomics England Curator)

Mode of inheritance for gene SLC6A19 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal

17 Sep 2024, Gel status: 3

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: SLC6A19 were set to 27604308; 20399395; 19335424

11 Jun 2024, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: SLC6A19 were changed from Hartnup disorder, OMIM:234500 to Hartnup disorder, OMIM:234500

11 Jun 2024, Gel status: 3

Set mode of inheritance

Achchuthan Shanmugasundram (Genomics England Curator)

Mode of inheritance for gene: SLC6A19 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

11 Jun 2024, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: SLC6A19 were changed from Hartnup disorder, OMIM:234500 to Hartnup disorder, OMIM:234500

11 Jun 2024, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: SLC6A19 were changed from Hartnup disorder, OMIM:234500 to Hartnup disorder, OMIM:234500

11 Jun 2024, Gel status: 3

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: SLC6A19 were changed from Iminoglycinuria, digenic; Hartnup disorder AD to Hartnup disorder, OMIM:234500

11 Jun 2024, Gel status: 3

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q2_24_NHS_review tag was added to gene: SLC6A19.

11 Jun 2024, Gel status: 3

Added Tag, Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q2_24_MOI tag was added to gene: SLC6A19. Tag Q2_24_expert_review tag was added to gene: SLC6A19.

13 Feb 2019, Gel status: 4

Added New Source, Added New Source

Ivone Leong (Genomics England Curator)

Source NHS GMS was added to SLC6A19. Source London North GLH was added to SLC6A19.

8 Jan 2019, Gel status: 4

Panel promoted to version 1.0

Ellen McDonagh (Genomics England Curator)

Ellen McDonagh: Comment on mode of pathogenici

16 Dec 2018, Gel status: 4

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

Ellen McDonagh (Genomics England Curator)

gene: SLC6A19 was added gene: SLC6A19 was added to Inborn errors of metabolism. Sources: Expert Review Green Mode of inheritance for gene: SLC6A19 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal Publications for gene: SLC6A19 were set to 27604308; 20399395; 19335424 Phenotypes for gene: SLC6A19 were set to Iminoglycinuria, digenic; Hartnup disorder AD