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Primary immunodeficiency

Gene: SLC29A3

Green List (high evidence)

SLC29A3 (solute carrier family 29 member 3)
EnsemblGeneIds (GRCh38): ENSG00000198246
EnsemblGeneIds (GRCh37): ENSG00000198246
OMIM: 612373, Gene2Phenotype
SLC29A3 is in 12 panels

5 reviews

Kimberly Gilmour (Great Ormond Street Hopsital)

Green List (high evidence)

agree with green gene
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Tracy Briggs (Manchester Genomic Medicine Centre)

Green List (high evidence)

YES- this is covered on our targeted exome
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Eleanor Williams (Genomics England Curator)

Green List (high evidence)

Comment on list classification: Changed rating of gene from Red to Green. This gene was rated as Green in v2.208 and incorrectly automatically demoted to Red in v2.209. This was due to a defect in the automatic PanelApp uploading tool when a set of publications was added to the panel with the source ‘Other’, and under certain conditions associated to previous sources listed, resulted in the rating of the gene being automatically changed when it should not have been.
Created: 14 Oct 2020, 4:24 p.m. | Last Modified: 14 Oct 2020, 4:24 p.m.
Panel Version: 2.310
The following PubMed IDs were added to entity SLC29A3: 20619369;20140240. These publications have been associated with OMIM phenotype MIM#602782, which is listed for this entity, by the autoinflammation subgroup of the Human Phenotype Ontology Immune Mediated Disorders Consortium (https://hpo-immune-mediated-disorders.groups.io/g/update) in August 2020.
Created: 13 Oct 2020, 9:36 a.m. | Last Modified: 13 Oct 2020, 9:36 a.m.
Panel Version: 2.208
Comment on publications: Publication from OMIM entry
Created: 10 May 2018, 2:37 p.m.
Comment on list classification: Cases from more than three families with plausible disease causing mutations.
Created: 10 May 2018, 2:25 p.m.
SLC29A3 is associated with Histiocytosis-lymphadenopathy plus syndrome in OMIM but not in Gene2Phenotype. It is a group of conditions with histiocytosis as a common feature (Genetics Home Reference). OMIM reports 14 variants in this gene associated with the disorder. Cases from more than three families with plausible disease causing mutations.
Created: 10 May 2018, 2:25 p.m.
Comment on phenotypes: Added MIM ID to Histiocytosis-lymphadenopathy plus syndrome
Created: 10 May 2018, 1:37 p.m.

Publications

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

Gene rating submitted by Kimberly Gilmour and Austen Worth on behalf of London North GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email 6th September the Specialist Test Group all agreed there is enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Gene rating submitted by Tracy Briggs, David Gokhale and Abigal Rousseau on behalf of North West GLH for the GMS Immunology specialist test group. As discussed with the GMS Immunology Specialist Test Group during webex call 28th March 2019 and confirmed in follow up email on 20th June the Specialist Test Group all agreed there is enough evidence to rate this gene Green.
Created: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): SLC29A3 .PanelApp HGNC gene symbol check: SLC29A3 . IUIS Disease: SLC29A3 mutation . IUIS Inheritance: AR .T cells: Increased activated T cells, .B cells: N/A, .IUIS Other affected cells: Leukocytes, bone cells. IUIS Associated features: Hyperpigmentation hypertrichosis, histiocytosis-lymphadenopathy plus syndrome . IUIS Major category: Autoinflammatory Disorders. IUIS Subcategory: Non-Inflammasome Related Conditions
Created: 2 Jul 2018, 10:35 a.m.
This gene was absent from the original PanelApp PID panel dataset (review April 2018). However it was listed in external expert immunodeficiency diagnostic gene list(s)
GOSH or GRID. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1.
Created: 19 Apr 2018, 3:10 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: SLC29A3, PanelApp HGNC gene symbol check: SLC29A3, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Autoinflammatory disorders / Other autoinflammatory diseases with known genetic defect / Other autoinflammatory diseases with known genetic defect
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: SLC29A3, GRID_Gene_Symbol: SLC29A3, GRID_Transcript_ENS_Community submitted: ENST00000373189, GRID_Transcript_RefSeq: NM_018344.5, GRID_Transcript_ENS_used_on_Production: ENST00000373189
Created: 17 Apr 2018, 12:12 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Other
  • NHS GMS
  • North West GLH
  • London North GLH
  • IUIS Classification February 2018
  • Victorian Clinical Genetics Services
  • ESID Registry 20171117
  • GRID V2.0
Phenotypes
  • Histiocytosis-lymphadenopathy plus syndrome 602782
  • Other autoinflammatory diseases with known genetic defect
  • Hyperpigmentation hypertrichosis, histiocytosis-lymphadenopathy plus syndrome
  • Autoinflammatory Disorders
OMIM
612373
Clinvar variants
Variants in SLC29A3
Penetrance
None
Publications
Panels with this gene

History Filter Activity

14 Oct 2020, Gel status: 3

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: slc29a3 has been classified as Green List (High Evidence).

13 Oct 2020, Gel status: 1

Added New Source, Set publications, Status Update

Eleanor Williams (Genomics England Curator)

Source Other was added to SLC29A3. Publications for gene SLC29A3 were updated from 16650224; 18940313; 20619369; 17461801; 19336477; 16155931; 20140240; 16118898; 21178579; 19175903; 9545394; 21888995; 23530176; 18947330; 22238637; 22653152; 22875837 to 17461801; 19336477; 23530176; 18940313; 22238637; 16118898; 22875837; 19175903; 21888995; 20140240; 16155931; 21178579; 9545394; 16650224; 22653152; 18947330; 20619369 Rating Changed from Green List (high evidence) to Red List (low evidence)

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to SLC29A3.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to SLC29A3.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to SLC29A3.

12 Jul 2018, Gel status: 4

Panel promoted to version 1.0

Louise Daugherty (Genomics England Curator)

2018-07-12 Louise Daugherty (Genomics England Curator) promoted panel to v1.0. Reviews were assessed, and panel was revised according to expert reviews and further in-house curation based on PanelApp guidelines. Previous panels (A- or hypo-gammaglobulinaemia, Congenital neutropaenia, Agranulocytosis, Combined B and T cell defect, Inherited complement deficiency and SCID panels) that were merged with this panel, were checked again for any changes/new reviews prior to versioning of this panel, these merged panels are now retired/made internal.

1 Jul 2018, Gel status: 4

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene SLC29A3 were set to Histiocytosis-lymphadenopathy plus syndrome 602782, Other autoinflammatory diseases with known genetic defect, Hyperpigmentation hypertrichosis, histiocytosis-lymphadenopathy plus syndrome, Autoinflammatory Disorders

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to SLC29A3. Panel: Primary immunodeficiency disorders

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Victorian Clinical Genetics Services was added to SLC29A3. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: slc29a3 has been classified as Green List (High Evidence).

10 May 2018, Gel status: 3

Set publications

Eleanor Williams (Genomics England Curator)

Publications for SLC29A3 were set to 16650224; 18940313; 20619369; 17461801; 19336477; 16155931; 20140240; 16118898; 21178579; 19175903; 9545394; 21888995; 23530176; 18947330; 22238637; 22653152; 22875837

10 May 2018, Gel status: 3

Gene classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

10 May 2018, Gel status: 2

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for SLC29A3 were set to Histiocytosis-lymphadenopathy plus syndrome 602782; Other autoinflammatory diseases with known genetic defect

19 Apr 2018, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

17 Apr 2018, Gel status: 1

Added New Source, Set penetrance

Louise Daugherty (Genomics England Curator)

ESID Registry 20171117 was added to SLC29A3. Panel: Primary immunodeficiency disorders Phenotypes for gene SLC29A3 were set to Histiocytosis-lymphadenopathy plus syndrome, Other autoinflammatory diseases with known genetic defect

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene SLC29A3 were set to Histiocytosis-lymphadenopathy plus syndrome

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

SLC29A3 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

SLC29A3 was created by Louise Daugherty