Primary immunodeficiency or monogenic inflammatory bowel disease

Gene: FAT4

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, 12:55 p.m. | Last Modified: 14 Oct 2020, 12:55 p.m.

Panel Version: 2.251

The following PubMed IDs were added to gene FAT4 (OMIM gene MIM#612411): 24056717;22469822;22473091;24913602. 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

• 24056717
• 22469822
• 22473091
• 24913602

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

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)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Hennekam-lymphangiectasia-lymphedema syndrome; Van Maldergem syndrome 2

Publications

• 24913602

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

Comment on list classification: Changed Amber to Green from external review comment and further publications to support gene-disease association.

Created: 3 Jul 2018, 12:16 p.m.

Hennekam syndrome is an inherited disorder resulting from malformation of the lymphatic system, which is part of both the circulatory system and immune system.

Created: 3 Jul 2018, 12:02 p.m.

Comment on publications: Added publications suggested from external expert review to support upgrading of the gene to Green

Created: 3 Jul 2018, 11:56 a.m.

Comment on phenotypes: added phenotype form OMIM and MIMid

Created: 3 Jul 2018, 11:56 a.m.

OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): FAT4 .PanelApp HGNC gene symbol check: FAT4 . IUIS Disease: Hennekam-lymphangiectasia-lymphedema syndrome due to FAT4 deficiency . IUIS Inheritance: AR .T cells: Normal, .B cells: Low/variable, .IUIS Other affected cells: N/A. IUIS Associated features: Lymphangiectasia and lymphedema with facial abnormalities and other dysmorphic features. IUIS Major category: Combined immunodeficiencies with associated or syndromic features. IUIS Subcategory: Other Combined immunodeficiencies with associated or syndromic features

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

Comment on list classification: This gene was absent from the original PanelApp PID panel dataset (review April 2018). However it was listed in external expert immunodeficiency diagnostic gene list from Victorian Clinical Genetics Services. In this combined PID panel, this gene has been rated as AMBER and needs further curational review to assess pertinence prior to v1. No disorder or MOI was listed in the submitted list.

Created: 26 Jun 2018, 12:46 p.m.