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Primary immunodeficiency or monogenic inflammatory bowel disease

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

7 reviews

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to green and the mode of inheritance set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted following NHS Genomic Medicine Service approval.
Created: 3 May 2024, 8:36 p.m. | Last Modified: 3 May 2024, 8:36 p.m.
Panel Version: 5.3

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

Comment on list classification: As reviewed by Hannah Knight, there is sufficient evidence available for the promotion of this gene to green rating in the next GMS review.
Created: 31 Oct 2023, 11:07 a.m. | Last Modified: 31 Oct 2023, 11:07 a.m.
Panel Version: 4.77

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
autoinflammatory syndrome, MONDO:0019751

Hannah Knight (NIHR BioResource - University of Cambridge)

Green List (high evidence)

PMID: 31874111 reported 6 patients with systemic autoinflammatory diseases, some diagnosed clinically with CANDLE syndrome. All had de novo frameshift variants which tightly cluster (p.I876Lfs*15; p.K878Sfs*13; p.F886Lfs*11; p.F889Sfs*2)
PMID: 36969289 then reported one additional patient with frameshift variant (p.F889Sfs*2)
Created: 13 Oct 2023, 8:52 a.m. | Last Modified: 13 Oct 2023, 8:52 a.m.
Panel Version: 4.41

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
SAMD9L-associated autoinflammatory disease

Publications

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

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

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

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.

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • 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
  • Bone marrow failure
  • Combined immunodeficiencies with associated or syndromic features
OMIM
611170
Clinvar variants
Variants in SAMD9L
Penetrance
None
Publications
Panels with this gene

History Filter Activity

3 May 2024, Gel status: 3

Removed Tag, Removed Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q4_23_promote_green was removed from gene: SAMD9L. Tag Q4_23_NHS_review was removed from gene: SAMD9L.

3 May 2024, Gel status: 3

Added New Source, Status Update

Achchuthan Shanmugasundram (Genomics England Curator)

Source Expert Review Green was added to SAMD9L. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

31 Oct 2023, Gel status: 2

Added Tag, Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q4_23_promote_green tag was added to gene: SAMD9L. Tag Q4_23_NHS_review tag was added to gene: SAMD9L.

31 Oct 2023, Gel status: 2

Entity classified by Genomics England curator

Achchuthan Shanmugasundram (Genomics England Curator)

Gene: samd9l has been classified as Amber List (Moderate Evidence).

31 Oct 2023, Gel status: 2

Set mode of inheritance

Achchuthan Shanmugasundram (Genomics England Curator)

Mode of inheritance for gene: SAMD9L was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

31 Oct 2023, Gel status: 2

Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Publications for gene: SAMD9L were set to 32048120; 28202457; 32086639

28 Feb 2020, Gel status: 2

Added New Source, Set Phenotypes, Set publications

Louise Daugherty (Genomics England Curator)

Source IUIS Classification December 2019 was added to SAMD9L. Added phenotypes Bone marrow failure; MDS, neurological features for gene: SAMD9L Publications for gene SAMD9L were updated from 28202457 to 32048120; 28202457; 32086639

26 Sep 2019, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: samd9l has been classified as Amber List (Moderate Evidence).

17 Sep 2019, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source North West GLH was added to SAMD9L.

17 Sep 2019, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to SAMD9L.

17 Sep 2019, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to SAMD9L.

12 Sep 2019, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: SAMD9L were set to

29 Mar 2019, Gel status: 1

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: SAMD9L was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

12 Jul 2018, Gel status: 1

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: 1

Set penetrance

Louise Daugherty (Genomics England Curator)

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

26 Jun 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

SAMD9L was added to Primary immunodeficiency disorders panel. Sources: IUIS Classification February 2018

26 Jun 2018, Gel status: 1

Created

Louise Daugherty (Genomics England Curator)

SAMD9L was created by Louise Daugherty