Primary immunodeficiency or monogenic inflammatory bowel disease

Gene: ORAI1

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, 1:38 p.m. | Last Modified: 14 Oct 2020, 1:38 p.m.

Panel Version: 2.289

The following PubMed IDs were added to gene ORAI1 (OMIM gene MIM#610277): 8814256;7798233;16582901. 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

Publications

• 8814256
• 7798233
• 16582901

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

Comment on list classification: Associated with phenotype in OMIM and not in Gen2Phen. At least 4 variants identified in 3 unrelated cases, together with supportive functional studies.

Created: 9 May 2018, 10:35 a.m.

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 review as there are sufficient cases with immune dysfunction in biallelic form, from the previous reviews, the previous Red rating was based upon delineation of the specific phenotypes for the specific panels. Therefore, Green rating is suitable for this panel that covers a immune dysfunction, not just SCID

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

OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): ORAI1 .PanelApp HGNC gene symbol check: ORAI1 . IUIS Disease: ORAI-1 deficiency . IUIS Inheritance: AR .T cells: N/A, .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: 20 Apr 2018, 12:25 p.m.

Original metadata downloaded from ESID Registry. ESID_Gene_original: Orai1 (TMEM142A), PanelApp HGNC gene symbol check: ORAI1, 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: ORAI1, GRID_Gene_Symbol: ORAI1, GRID_Transcript_ENS_Community submitted: ENST00000330079, GRID_Transcript_RefSeq: NM_032790.3, GRID_Transcript_ENS_used_on_Production: ENST00000330079

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

Red List (low evidence)

Comment on list classification: After feedback from reviewers, gene should remain on the red list.

Created: 20 May 2016, 2:18 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

There are 2 publications with 3 different sets of mutations/families so although rare I would make this an amber which we don't seem to have an option of as we review. I agree with Sophie not so much SCID as CID...

Created: 20 Oct 2015, 1:42 p.m.

Green List (high evidence)

As stated below, there is good evidence that AR mutations in this gene cause immunodeficiency

Created: 23 Oct 2019, 6:42 a.m. | Last Modified: 23 Oct 2019, 6:42 a.m.

Panel Version: 1.132

There is good evidence that AR mutations in this gene cause immune dysfunction but not SCID

Created: 19 Oct 2015, 5:45 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
immunodeficiency, ectodermal dysplasia and myopathy

Publications

• 16582901
• 20004786