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STRs in panel
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COVID-19 research

Gene: LYST

Green List (high evidence)

LYST (lysosomal trafficking regulator)
EnsemblGeneIds (GRCh38): ENSG00000143669
EnsemblGeneIds (GRCh37): ENSG00000143669
OMIM: 606897, Gene2Phenotype
LYST is in 25 panels

5 reviews

Kimberly Gilmour (Great Ormond Street Hopsital)

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

Tracy Briggs (Manchester Genomic Medicine Centre)

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

Sophie Hambleton (Newcastle University)

Green List (high evidence)

Sarah Leigh (Genomics England Curator)

Comment on phenotypes: Chediak-Higashi syndrome 214500
Created: 30 Apr 2018, 1:49 p.m.
Comment on list classification: Associated with relevant phenotypes in OMIM and as confirmed Gen2Phen gene. At least 10 biallelic variants reported in unrelated cases, seven in childhood onset Chediak-Higashi syndrome 214500 and three in adult onset cases.
Created: 30 Apr 2018, 1:49 p.m.

Louise Daugherty (Genomics England Curator)

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
OriginaI Metadata from IUIS classification table (February, 2018) downloaded 20180614. IUIS Genetic defect (original gene symbol in IUIS download): LYST .PanelApp HGNC gene symbol check: LYST . IUIS Disease: Chediak-Higashi syndrome . IUIS Inheritance: AR .T cells: N/A, .B cells: Normal, .IUIS Other affected cells: N/A. IUIS Associated features: Partial albinism, recurrent infections, fever, HSM, HLH, giant lysosomes, neutropenia, cytopenias, bleeding tendency, progressive neurological dysfunction. IUIS Major category: Diseases of Immune Dysregulation. IUIS Subcategory: FHL Syndromes with Hypopigmentation
Created: 2 Jul 2018, 10:35 a.m.
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(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: LYST, PanelApp HGNC gene symbol check: LYST, ESID classification: Main_category/ Sub_category/ PID_Diagnosis Diseases of immune dysregulation / Hemophagocytic Lymphohistiocytosis (HLH) / Chediak Higashi syndrome
Created: 17 Apr 2018, 12:29 p.m.
Original metadata supplied by GRID. GRID Gene Symbol HGNC PanelApp check: LYST, GRID_Gene_Symbol: LYST, GRID_Transcript_ENS_Community submitted: ENST00000389794, GRID_Transcript_RefSeq: NM_000081.3, GRID_Transcript_ENS_used_on_Production: ENST00000389794
Created: 17 Apr 2018, 12:12 p.m.

History Filter Activity

1 Apr 2020, Gel status: 3

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Ellen McDonagh (Genomics England Curator)

gene: LYST was added gene: LYST was added to Viral susceptibility. Sources: Expert Review Green,ESID Registry 20171117,North West GLH,Victorian Clinical Genetics Services,GRID V2.0,NHS GMS,GOSH PID v.8.0,London North GLH,IUIS Classification February 2018 Mode of inheritance for gene: LYST was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LYST were set to 9215679; 9215680; 10482950; 8896560 Phenotypes for gene: LYST were set to Chediak-Higashi syndrome 214500; Chediak Higashi syndrome; Partial albinism, recurrent infections, fever, HSM, HLH, giant lysosomes, neutropenia, cytopenias, bleeding tendency, progressive neurological dysfunction; Diseases of Immune Dysregulation