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Likely inborn error of metabolism v5.5 SLC6A19 Achchuthan Shanmugasundram Added comment: 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.
Likely inborn error of metabolism v5.3 SLC6A20 Achchuthan Shanmugasundram Tag Q4_23_demote_red was removed from gene: SLC6A20.
Tag Q4_23_expert_review was removed from gene: SLC6A20.
Likely inborn error of metabolism v5.3 SLC6A20 Sarah Leigh commented on gene: SLC6A20: The rating of this gene has been updated to red following NHS Genomic Medicine Service approval. Comment from GMS: 'Demotion of a green gene - disease association refuted in OMIM, as the single variant has been classified as common in gnomAD database.'
Likely inborn error of metabolism v5.2 SLC6A20 Achchuthan Shanmugasundram Source Expert Review Red was added to SLC6A20.
Source NHS GMS was added to SLC6A20.
Rating Changed from Green List (high evidence) to Red List (low evidence)
Likely inborn error of metabolism v4.122 SLC6A20 Achchuthan Shanmugasundram Tag Q4_23_expert_review tag was added to gene: SLC6A20.
Likely inborn error of metabolism v4.55 SLC6A20 Eleanor Williams commented on gene: SLC6A20: Added the gene-checked tag as this is the right gene on the panel, even though it probably should be demoted.
Likely inborn error of metabolism v4.55 SLC6A20 Eleanor Williams Tag gene-checked tag was added to gene: SLC6A20.
Likely inborn error of metabolism v4.52 SLC6A20 Sarah Leigh Tag refuted tag was added to gene: SLC6A20.
Tag Q4_23_demote_red tag was added to gene: SLC6A20.
Likely inborn error of metabolism v4.52 SLC6A20 Sarah Leigh edited their review of gene: SLC6A20: Added comment: 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).; Changed rating: RED; Changed phenotypes to: Hyperglycinuria 138500, Iminoglycinuria, digenic 242600
Likely inborn error of metabolism v4.52 SLC6A20 Eleanor Williams commented on gene: SLC6A20
Likely inborn error of metabolism v0.4 SLC6A20 Ellen McDonagh gene: SLC6A20 was added
gene: SLC6A20 was added to Inborn errors of metabolism. Sources: Expert Review Green
Mode of inheritance for gene: SLC6A20 was set to BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Publications for gene: SLC6A20 were set to 24816252; 19033659
Phenotypes for gene: SLC6A20 were set to Hyperglycinuria