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Arthrogryposis

Gene: SLC6A9

Amber List (moderate evidence)

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

3 reviews

Arina Puzriakova (Genomics England Curator)

Comment on list classification: There is now sufficient evidence to promote this gene to Green at the next GMS panel update (added 'Q4_21_rating' tag)
Created: 3 Nov 2021, 3:51 p.m. | Last Modified: 3 Nov 2021, 3:51 p.m.
Panel Version: 3.140

Rhiannon Mellis (Great Ormond Street Hospital)

Green List (high evidence)

Review cc'd from Fetal Anomalies panel. New publications since last review on arthrogryposis panel.

This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs.

Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH).

Outcome of review: Confirmed that the phenotype is fetally relevant, support adding to the Fetal anomalies panel as a Green gene.

Details of review:
Dempsey et al 2020 (PMID: 31875334) report a fetus with persistently raised NT, hyperextended legs, unilateral talipes. Flexed arms. Small stomach. Consanguineous family. Other reports of SLC6A9 causing arthrogryposis multiplex congenita (presenting prenatally) include: Kurolap et al 2016, PMID: 27773429 (2 families); Hauf et al 2020, PMID: 32712301 (1 family); Mademont-Soler et al 2021, PMID: 33269555 (1 family)
Created: 29 Oct 2021, 2:22 p.m. | Last Modified: 29 Oct 2021, 2:22 p.m.
Panel Version: 3.137

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Arthrogryposis multiplex congenita; Glycine encephalopathy

Publications

Rebecca Foulger (Genomics England curator)

I don't know

Comment on list classification: Rated SLC6A9 Amber in consultation with Zerin Hyder (Genomics England Clinical Team) based on literature cases (PMIDs 27773429, 27481395), and a Probable rating for an Arthrogryposis disorder in Gene2Phenotype.
Created: 26 Nov 2019, 4:16 p.m. | Last Modified: 26 Nov 2019, 4:16 p.m.
Panel Version: 2.67
Gene2Phenotype phenotype of 'Glycine Encephalopathy with Arthrogryposis' with 'probable' disease confidence based on PMID:27773429 (Kurolap et al., 2016) who report 4 individuals from 2 Arab-Muslim families with arthrogryposis amongst their symptoms. In addition, PMID:27481395 (Alfadhel et al., 2016) report a consanguineous family with one child who presented with non-ketotic hyperglycinemia and a homozygous missense variant in SLC6A9 (p.Ser407Gly). Features included joint laxity but Arthrogryposis isn't mentioned specifically.
Created: 26 Nov 2019, 3:19 p.m. | Last Modified: 26 Nov 2019, 3:19 p.m.
Panel Version: 2.64
Added to Arthrogryposis panel after agreement with Zerin Hyder (Genomics England Clinical Team), based on Arthrogryposis phenotype on DDG2P panel V1.154.
Created: 26 Nov 2019, 3:16 p.m. | Last Modified: 26 Nov 2019, 3:19 p.m.
Panel Version: 2.64

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Other
  • Literature
Phenotypes
  • Glycine encephalopathy with normal serum glycine, OMIM:617301
Tags
Q4_21_rating Q4_21_NHS_review
OMIM
601019
Clinvar variants
Variants in SLC6A9
Penetrance
None
Publications
Panels with this gene

History Filter Activity

13 Dec 2021, Gel status: 2

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag Q4_21_NHS_review tag was added to gene: SLC6A9.

3 Nov 2021, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: slc6a9 has been classified as Amber List (Moderate Evidence).

3 Nov 2021, Gel status: 2

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: SLC6A9 were set to 27773429; 27481395

3 Nov 2021, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: SLC6A9 were changed from Glycine encephalopathy with normal serum glycine, 617301; Glycine Encephalopathy with Arthrogryposis to Glycine encephalopathy with normal serum glycine, OMIM:617301

3 Nov 2021, Gel status: 2

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag Q4_21_rating tag was added to gene: SLC6A9.

26 Nov 2019, Gel status: 2

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: slc6a9 has been classified as Amber List (Moderate Evidence).

26 Nov 2019, Gel status: 1

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: SLC6A9 were set to

26 Nov 2019, Gel status: 1

Added New Source, Status Update

Rebecca Foulger (Genomics England curator)

Source Expert Review Red was added to SLC6A9. Rating Changed from Green List (high evidence) to Red List (low evidence)

26 Nov 2019, Gel status: 3

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

Rebecca Foulger (Genomics England curator)

gene: SLC6A9 was added gene: SLC6A9 was added to Arthrogryposis. Sources: Literature,Other,Expert Review Green Mode of inheritance for gene: SLC6A9 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: SLC6A9 were set to Glycine encephalopathy with normal serum glycine, 617301; Glycine Encephalopathy with Arthrogryposis