Research panel - Severe Paediatric Disorders
Gene: SLC6A19

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

3 reviews

Sarah Leigh (Genomics England Curator)

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.
Achchuthan Shanmugasundram (Genomics England Curator), 11 Jun 2024
Created: 17 Sep 2024, 2:38 p.m. | Last Modified: 17 Sep 2024, 2:38 p.m.

Panel Version: 1.195

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Created: 17 Sep 2024, 2:38 p.m.
Last Modified: 17 Sep 2024, 2:38 p.m.
Panel version: 1.195

Tracy Lester (Genetics laboratory, Oxford UK)

Green List (high evidence)

I can't see any evidence that this gene is associated with an autosomal dominant phenotype and suggest the MOI be changed to biallelic only.
Created: 21 Jul 2023, 8:34 a.m. | Last Modified: 21 Jul 2023, 8:34 a.m.

Panel Version: 1.159

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
pellagra; cerebellar ataxia; psychosis

Publications

32644502

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

Created: 21 Jul 2023, 8:34 a.m.
Last Modified: 21 Jul 2023, 8:34 a.m.
Panel version: 1.159

Louise Daugherty (Genomics England Curator)

I don't know

Initial gene list (NGC_genelist-20190823_GREEN_dis_moi_forCuration_20200211.xlsx) collated by Dr Courtney French (University of Cambridge University Hospital NHS Foundation), Dr Karyn Megy (Clinical Feedback Lead, NIHR BioResource - Rare Diseases Study, University of Cambridge University Hospital NHS Foundation), Dr Alba Sanchis-Juan (NIHR BioResource - Rare Diseases Study, University of Cambridge University Hospital NHS Foundation) and Lucy Raymond (Professor of Medical Genetics and Neurodevelopment, University of Cambridge University Hospital NHS Foundation). Submitted to the PanelApp resource January 2020 on behalf of the Next Generation Children Project, Addenbrookes' Hospital, Cambridge. Gene Symbol submitted: SLC6A19; Recommended initial gene rating: Green List (high evidence); Phenotypes: Hartnup disorder, 234500 (3) | Hyperglycinuria, 138500 (3) | Iminoglycinuria, digenic, 242600 (3); Mode of inheritance: Autosomal recessive | Autosomal dominant | Autosomal recessive, Digenic recessive
Created: 20 Feb 2020, 5:25 p.m. | Last Modified: 20 Feb 2020, 5:25 p.m.

Panel Version: 0.12

Created: 20 Feb 2020, 5:25 p.m.
Last Modified: 20 Feb 2020, 5:25 p.m.
Panel version: 0.12

Details

Mode of Inheritance

BIALLELIC, autosomal or pseudoautosomal

Sources

Next Generation Children Project
Expert Review Green
Expert list

Phenotypes

Iminoglycinuria, digenic, 242600
Hyperglycinuria, 138500
Hartnup disorder, 234500

OMIM

608893

Clinvar variants

Variants in SLC6A19

Penetrance

None

Publications

Panels with this gene

History Filter Activity

17 Sep 2024, Gel status: 3

Set mode of inheritance

Sarah Leigh (Genomics England Curator)

Mode of inheritance for gene: SLC6A19 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown 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 30847515

17 Sep 2024, Gel status: 3

Set mode of inheritance

Sarah Leigh (Genomics England Curator)

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

20 Feb 2020, Gel status: 3