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COVID-19 research

Gene: SAMD9L

Green List (high evidence)
SAMD9L (sterile alpha motif domain containing 9 like)
EnsemblGeneIds (GRCh38): ENSG00000177409
EnsemblGeneIds (GRCh37): ENSG00000177409
OMIM: 611170, Gene2Phenotype
SAMD9L is in 11 panels

4 reviews

Sophie Hambleton (Newcastle University)

Agree with amber rating for now
Created: 23 Oct 2019, 7:12 a.m. | Last Modified: 23 Oct 2019, 7:12 a.m.
Panel Version: 1.132
Created: 23 Oct 2019, 7:12 a.m.
Last Modified: 23 Oct 2019, 7:12 a.m.
Panel version: Imported from Primary immunodeficiency panel version 1.132

Kimberly Gilmour (Great Ormond Street Hopsital)

I don't know

agree with all the Amber genes
Created: 25 Sep 2019, 1:49 p.m. | Last Modified: 25 Sep 2019, 1:49 p.m.
Panel Version: 1.115
Created: 25 Sep 2019, 1:49 p.m.
Last Modified: 25 Sep 2019, 1:49 p.m.
Panel version: Imported from Primary immunodeficiency panel version 1.115

Tracy Briggs (Manchester Genomic Medicine Centre)

I don't know

The amber genes are covered on our targeted exome, we feel that these should be covered in the testing
Created: 25 Sep 2019, 1:44 p.m. | Last Modified: 25 Sep 2019, 1:44 p.m.
Panel Version: 1.114
Created: 25 Sep 2019, 1:44 p.m.
Last Modified: 25 Sep 2019, 1:44 p.m.
Panel version: Imported from Primary immunodeficiency panel version 1.114

Louise Daugherty (Genomics England Curator)

I don't know

Ataxia pancytopaenia syndrome - 2 unrelated families, no functional work - amber association, is there an immunological phenotype?
Created: 26 Sep 2019, 3:59 p.m. | Last Modified: 26 Sep 2019, 3:59 p.m.
Panel Version: 1.130
Comment on list classification: Changed rating from Red to Amber to reflect the agreed rating agreed by the GMS Immunology Specialist Test Group
Created: 26 Sep 2019, 10:55 a.m. | Last Modified: 26 Sep 2019, 10:55 a.m.
Panel Version: 1.123
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 only enough evidence to rate this gene Amber.
Created: 25 Sep 2019, 3 p.m. | Last Modified: 25 Sep 2019, 3 p.m.
Panel Version: 1.116
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 only enough evidence to rate this gene Amber
Created: 25 Sep 2019, 3 p.m. | Last Modified: 25 Sep 2019, 3 p.m.
Panel Version: 1.116
Comment on publications: Added PMID: 28202457 Tesi et al, Gain of function SAMD9L muttaiosn caise a syndorme of cytopenaia, immunodefiency, MDS and neurological symptoms BLOOD, 2017, 2266-2279 suggested by Kimberly Gilmour (LNGLH) on behalf of the Specialist Test Group to support inclusion of this gene on the panel and a Amber rating.
Created: 12 Sep 2019, 4:01 p.m. | Last Modified: 12 Sep 2019, 4:01 p.m.
Panel Version: 1.57
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): SAMD9L .PanelApp HGNC gene symbol check: SAMD9L . IUIS Disease: SAMD9L . IUIS Inheritance: AD (GOF) .T cells: N/A, .B cells: Low, .IUIS Other affected cells: N/A. IUIS Associated features: Cytopenia, predisposition to MDS with chromosome 7 aberrations, immunodeficiency, and progressive cerebellar dysfunction. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: DyskeratosIs Congenita (DKC), Myelodysplasia, Short Telomeres
Created: 6 Jul 2018, 12:35 p.m.
Created: 6 Jul 2018, 12:35 p.m.

Panel version: Imported from Primary immunodeficiency panel version 1.130

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
  • IUIS Classification February 2018
  • IUIS Classification December 2019
  • London North GLH
  • NHS GMS
  • North West GLH
  • IUIS Classification December 2019
  • North West GLH
  • London North GLH
  • NHS GMS
  • IUIS Classification February 2018
Phenotypes
  • Cytopenia, predisposition to MDS with chromosome 7 aberrations, immunodeficiency, and progressive cerebellar dysfunction
  • MDS, neurological features
  • Combined immunodeficiencies with associated or syndromic features
  • Bone marrow failure
OMIM
611170
Clinvar variants
Variants in SAMD9L
Penetrance
None
Publications
Panels with this gene

History Filter Activity

2 Apr 2020, Gel status: 3

Added New Source, Set Phenotypes, Status Update

Ellen McDonagh (Genomics England Curator)

Source Expert Review Green was added to SAMD9L. Added phenotypes Cytopenia, predisposition to MDS with chromosome 7 aberrations, immunodeficiency, and progressive cerebellar dysfunction; Combined immunodeficiencies with associated or syndromic features; MDS, neurological features; Bone marrow failure for gene: SAMD9L Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

1 Apr 2020, Gel status: 2

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

Ellen McDonagh (Genomics England Curator)

gene: SAMD9L was added gene: SAMD9L was added to Viral susceptibility. Sources: North West GLH,NHS GMS,London North GLH,IUIS Classification December 2019,IUIS Classification February 2018,Expert Review Amber Mode of inheritance for gene: SAMD9L was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: SAMD9L were set to 32086639; 32048120; 28202457 Phenotypes for gene: SAMD9L were set to Cytopenia, predisposition to MDS with chromosome 7 aberrations, immunodeficiency, and progressive cerebellar dysfunction; Combined immunodeficiencies with associated or syndromic features; MDS, neurological features; Bone marrow failure