Primary immunodeficiency or monogenic inflammatory bowel disease

Gene: STIM1

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

Green List (high evidence)

Comment on list classification: Changed rating of gene from Red to Green. This gene was rated as Green in v2.208 and incorrectly automatically demoted to Red in v2.209. This was due to a defect in the automatic PanelApp uploading tool when a set of publications was added to the panel with the source ‘Other’, and under certain conditions associated to previous sources listed, resulted in the rating of the gene being automatically changed when it should not have been.

Created: 14 Oct 2020, 4:28 p.m. | Last Modified: 14 Oct 2020, 4:28 p.m.

Panel Version: 2.316

The following PubMed IDs were added to gene STIM1 (OMIM gene MIM#605921): 24570283;22190180;20876309;19420366. These publications have been associated with the gene by the immunodeficiencies subgroup of the Human Phenotype Ontology Immune Mediated Disorders Consortium (https://hpo-immune-mediated-disorders.groups.io/g/update) in August 2020.

Created: 13 Oct 2020, 9:36 a.m. | Last Modified: 13 Oct 2020, 9:36 a.m.

Panel Version: 2.208

Comment on list classification: Changing this gene from Amber to Green as there are >3 independant cases providing association of this gene and the disorder

Created: 3 May 2018, 10 p.m.

STIM1 is associated with Immunodeficiency 10 in OMIM. OMIM lists 5 publications reporting STIM1 variants in patients with immunodeficiency; Picard et al. (2009) (PMID: 19420366), Byun et al. (2010) (PMID: 20876309), Fuchs et al. (2012) (PMID: 22190180), Wang et al. (2014) (PMID: 24621671), Parry et al. (2016) (PMID: 26560041) . No relevant disease association with this gene in Gene2Phenotype. Orphanet: the gene is associated with Combined immunodeficiency due to STIM1 deficiency (ORPHA:317430) and it states 'To date, it has been reported in 4 patients from two families.' Rating this gene as green as > 3 cases where a likely disease causing variant is found.

Created: 2 May 2018, 2:33 p.m.

Comment on phenotypes: Added MIM number to Immunodeficiency 10

Created: 2 May 2018, 2:05 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Combined immunodeficiency due to STIM1 deficiency ORPHA:317430

Publications

• 24570283
• 22190180
• 20876309
• 19420366

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

Green rating as there are sufficient cases with an immune phenotype, prior historic red ratings are due to SCID specific panel

Created: 10 Jul 2018, 4:12 p.m.

OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): STIM1 .PanelApp HGNC gene symbol check: STIM1 . IUIS Disease: STIM1 deficiency . IUIS Inheritance: AR .T cells: Variable, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Autoimmunity, EDA, non-progressive myopathy. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: Calcium Channel Defects

Created: 2 Jul 2018, 10:35 a.m.

This gene was present in the original PanelApp PID panel dataset (review in April 2018) rated as Red. The gene is present in the 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, 2:06 p.m.

Original metadata downloaded from ESID Registry. ESID_Gene_original: STIM1, PanelApp HGNC gene symbol check: STIM1, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Combined immunodeficiencies / Combined immunodeficiency (CID) / Combined immunodeficiency

Created: 17 Apr 2018, 12:29 p.m.

Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: STIM1, GRID_Gene_Symbol: STIM1, GRID_Transcript_ENS_Community submitted: ENST00000300737, GRID_Transcript_RefSeq: NM_003156.3, GRID_Transcript_ENS_used_on_Production: ENST00000300737

Created: 17 Apr 2018, 12:12 p.m.

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

Red List (low evidence)

Red List (low evidence)

Mutations in this gene do not cause SCID

Created: 19 Oct 2015, 7:53 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal