Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: SAMD9L
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
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
Agree with amber rating for nowCreated: 23 Oct 2019, 7:12 a.m. | Last Modified: 23 Oct 2019, 7:12 a.m.
Panel Version: 1.132
agree with all the Amber genesCreated: 25 Sep 2019, 1:49 p.m. | Last Modified: 25 Sep 2019, 1:49 p.m.
Panel Version: 1.115
The amber genes are covered on our targeted exome, we feel that these should be covered in the testingCreated: 25 Sep 2019, 1:44 p.m. | Last Modified: 25 Sep 2019, 1:44 p.m.
Panel Version: 1.114
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 GroupCreated: 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 AmberCreated: 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 TelomeresCreated: 6 Jul 2018, 12:35 p.m.
Tag Q4_23_promote_green tag was added to gene: SAMD9L. Tag Q4_23_NHS_review tag was added to gene: SAMD9L.
Gene: samd9l has been classified as Amber List (Moderate Evidence).
Mode of inheritance for gene: SAMD9L was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: SAMD9L were set to 32048120; 28202457; 32086639
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
Gene: samd9l has been classified as Amber List (Moderate Evidence).
Source North West GLH was added to SAMD9L.
Source London North GLH was added to SAMD9L.
Source NHS GMS was added to SAMD9L.
Publications for gene: SAMD9L were set to
Mode of inheritance for gene: SAMD9L was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
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.
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
SAMD9L was added to Primary immunodeficiency disorders panel. Sources: IUIS Classification February 2018
SAMD9L was created by Louise Daugherty