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COVID-19 research

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 15 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: 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
Phenotypes
  • Folate malabsorption, hereditary 229050
  • Congenital defect of folate absorption
  • Megaloblastic anemia, failure to thrive, if untreated for prolonged periods results in intellectual disability
  • Defects of Vitamin B12 and Folate metabolism
  • Combined immunodeficiencies with associated or syndromic features
OMIM
611672
Clinvar variants
Variants in SLC46A1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

1 Apr 2020, Gel status: 3

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

Ellen McDonagh (Genomics England Curator)

gene: SLC46A1 was added gene: SLC46A1 was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,London North GLH,IUIS Classification February 2018 Mode of inheritance for gene: SLC46A1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC46A1 were set to 17446347; 17129779; 27664775 Phenotypes for gene: SLC46A1 were set to Folate malabsorption, hereditary 229050; Congenital defect of folate absorption; Megaloblastic anemia, failure to thrive, if untreated for prolonged periods results in intellectual disability; Defects of Vitamin B12 and Folate metabolism; Combined immunodeficiencies with associated or syndromic features