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22q11.2 recurrent (DGS/VCFS) region (proximal, A-B) (includes TBX1) Loss
ISCA-37433-Loss 3
22q11.2 recurrent (DGS/VCFS) region (proximal, A-D) (includes TBX1) Loss
ISCA-37446-Loss 2

Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: SAMD9L

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

Created: 3 May 2024, 8:36 p.m.
Last Modified: 3 May 2024, 8:36 p.m.
Panel version: 5.3

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

Created: 31 Oct 2023, 11:06 a.m.
Last Modified: 31 Oct 2023, 11:06 a.m.
Panel version: 4.75

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

Created: 13 Oct 2023, 8:52 a.m.
Last Modified: 13 Oct 2023, 8:52 a.m.
Panel version: 4.41

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: 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: 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: 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: 1.130

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