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Primary immunodeficiency

Gene: SLC46A1

Green List (high evidence)

SLC46A1 (solute carrier family 46 member 1)
EnsemblGeneIds (GRCh38): ENSG00000076351
EnsemblGeneIds (GRCh37): ENSG00000076351
OMIM: 611672, Gene2Phenotype
SLC46A1 is in 14 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: 2.311
The following PubMed IDs were added to gene SLC46A1 (OMIM gene MIM#611672): 17446347;17129779. These publications have been associated with the gene by the immunodeficiencies 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 list classification: Rating this gene green as there are more than 3 cases of pathogenic mutations associated with the phenotype.
Created: 16 May 2018, 8:23 a.m.
Comment on phenotypes: Added MIM number to "Folate malabsorption, hereditary" and added the alternative name of "Congenital defect of folate absorption"
Created: 16 May 2018, 8:22 a.m.
In OMIM this gene is associated with Folate malabsorption, hereditary. Phenotypes associated with this disease include Recurrent infections, Increased susceptibility to pneumocystis and cytomegalovirus infections andHypoimmunoglobulinemia. OMIM reports that in affected members of a family with hereditary folate malabsorption, Qiu et al. (2006) (PMID: 17129779) identified a homozygous mutation in the SLC46A1 gene. OMIM also reports that in 5 infants with hereditary folate malabsorption, Zhao et al. (2007) (PMID: 17446347) identified 6 different biallelic mutations in the SLC46A1 gene. Clinvar reports 17 pathogenic SNVs in this gene associated with "Congenital defect of folate absorption". Zhou et al 2017 (PMID: 27664775) lists a recent table of variants associated with hereditary folate malabsorption. Rating this gene green as there are more than 3 cases of pathogenic mutations associated with the phenotype.
Created: 16 May 2018, 8:21 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

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): SLC46A1 .PanelApp HGNC gene symbol check: SLC46A1 . IUIS Disease: SLC46A1/PCFT deficiency causing hereditary folate malabsorbtion . IUIS Inheritance: AR .T cells: Low CD8, Nl CD4, absent MHC I on lymphocytes, .B cells: Variable, .IUIS Other affected cells: N/A. IUIS Associated features: Megaloblastic anemia, failure to thrive, if untreated for prolonged periods results in intellectual disability. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: Defects of Vitamin B12 and Folate Metabolism
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, 3:08 p.m.
Original metadata downloaded from ESID Registry. ESID_Gene_original: SLC46A1, PanelApp HGNC gene symbol check: SLC46A1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Other well defined PIDs / Defects of Vitamin B12 and Folate metabolism / Defects of Vitamin B12 and Folate metabolism
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: SLC46A1, GRID_Gene_Symbol: SLC46A1, GRID_Transcript_ENS_Community submitted: ENST00000440501, GRID_Transcript_RefSeq: NM_080669.3, GRID_Transcript_ENS_used_on_Production: ENST00000440501
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
  • Folate malabsorption, hereditary 229050
  • Defects of Vitamin B12 and Folate metabolism
  • Congenital defect of folate absorption
  • Megaloblastic anemia, failure to thrive, if untreated for prolonged periods results in intellectual disability
  • Combined immunodeficiencies with associated or syndromic features
OMIM
611672
Clinvar variants
Variants in SLC46A1
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: slc46a1 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 SLC46A1. Publications for gene SLC46A1 were updated from 17129779; 17446347; 27664775 to 17129779; 27664775; 17446347 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 SLC46A1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to SLC46A1.

17 Sep 2019, Gel status: 3

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to SLC46A1.

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 SLC46A1 were set to Folate malabsorption, hereditary 229050, Defects of Vitamin B12 and Folate metabolism, Congenital defect of folate absorption, Megaloblastic anemia, failure to thrive, if untreated for prolonged periods results in intellectual disability, Combined immunodeficiencies with associated or syndromic features

26 Jun 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

IUIS Classification February 2018 was added to SLC46A1. 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 SLC46A1. Panel: Primary immunodeficiency disorders

13 Jun 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: slc46a1 has been classified as Green List (High Evidence).

13 Jun 2018, Gel status: 3

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: SLC46A1 were set to 17129779; 17446347; 27664775

13 Jun 2018, Gel status: 3

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: SLC46A1 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal

16 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).

16 May 2018, Gel status: 2

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for SLC46A1 were set to Folate malabsorption, hereditary 229050; Defects of Vitamin B12 and Folate metabolism; Congenital defect of folate absorption

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 SLC46A1. Panel: Primary immunodeficiency disorders Phenotypes for gene SLC46A1 were set to Folate malabsorption, hereditary, Defects of Vitamin B12 and Folate metabolism

17 Apr 2018, Gel status: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

Phenotypes for gene SLC46A1 were set to Folate malabsorption, hereditary

17 Apr 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

SLC46A1 was added to Primary immunodeficiency disorders panel. Sources: GRID V2.0

17 Apr 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

SLC46A1 was created by Louise Daugherty