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Intellectual disability

Gene: SLC6A9

Green List (high evidence)

SLC6A9 (solute carrier family 6 member 9)
EnsemblGeneIds (GRCh38): ENSG00000196517
EnsemblGeneIds (GRCh37): ENSG00000196517
OMIM: 601019, Gene2Phenotype
SLC6A9 is in 5 panels

3 reviews

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

As a result of watchlist tag audit the watchlist tag was removed from SLC6A9- this is now a green gene with sufficient evidence/review
Created: 13 Jan 2020, 4:14 p.m. | Last Modified: 13 Jan 2020, 4:14 p.m.
Panel Version: 3.0
Comment on publications: added missing publication
Created: 19 Dec 2017, 4:53 p.m.

Arianna Tucci (Genomics England Curator)

Comment on list classification: Marked as green after literature review: there is enough evidence for the gene to be marked as green, and though the phenotype is very severe, the patients do have global developmental delay. Hence, upgraded to green
Created: 10 Nov 2017, 4:15 p.m.

Rebecca Foulger (Genomics England curator)

I don't know

Rated as Amber after clinical agreement from Arianna Tucci. Sufficient cases (3 unrelated reports) to link SLC6A9 with MIM:617301, but ID link is less clear. PMID:27481395 (2016) report a 15-month-old girl born of consanguineous Saudi parents with severe global developmental delay and a novel homozygous missense variant in the SLC6A9 gene: NM_201649.3: c.1219 A>G (p.Ser407Gly). Both parents and elder sister were heterozygous for this variant. PMID:27773429 (2016) report 4 children from 2 unrelated consanguineous Arab-Muslim families: age 2, the only survivor had significant global developmental delay and harbours variant c.928_932delAAGTC (p.Lys310Phefs*31) in SLC6A9.
Created: 31 Oct 2017, 9:23 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Glycine encephalopathy with normal serum glycine, 617301; Glycine encephalopathy and global developmental delay



Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
  • Expert Review Green
  • Glycine encephalopathy with normal serum glycine, 617301
  • Glycine encephalopathy and global developmental delay
Clinvar variants
Variants in SLC6A9
Panels with this gene

History Filter Activity

13 Jan 2020, Gel status: 3

Removed Tag

Louise Daugherty (Genomics England Curator)

Tag watchlist was removed from gene: SLC6A9.

12 Mar 2018, Gel status: 4

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

19 Dec 2017, Gel status: 4

Set publications

Louise Daugherty (Genomics England Curator)

Publications for SLC6A9 were set to 27481395; 27773429

29 Nov 2017, Gel status: 4

Added New Source

Ellen McDonagh (Genomics England Curator)

SLC6A9 was added to Intellectual disability panel. Sources: Expert Review Green

29 Nov 2017, Gel status: 4


Ellen McDonagh (Genomics England Curator)

SLC6A9 was created by Ellen McDonagh