Primary immunodeficiency or monogenic inflammatory bowel disease
Gene: LYSTEnsemblGeneIds (GRCh38): ENSG00000143669
EnsemblGeneIds (GRCh37): ENSG00000143669
OMIM: 606897, Gene2Phenotype
LYST is in 24 panels
6 reviews
Eleanor Williams (Genomics England Curator)
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, 1:19 p.m. | Last Modified: 14 Oct 2020, 1:19 p.m.
Panel Version: 2.274
The following PubMed IDs were added to entity LYST: 26944273;18043242;29939658;8717042. These publications have been associated with OMIM phenotype MIM#214500, which is listed for this entity, by the immunedysregulation 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
Kimberly Gilmour (Great Ormond Street Hopsital)
agree with green geneCreated: 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)
YES- this is covered on our targeted exomeCreated: 17 Sep 2019, 3:18 p.m. | Last Modified: 17 Sep 2019, 3:18 p.m.
Panel Version: 1.94
Sophie Hambleton (Newcastle University)
Sarah Leigh (Genomics England Curator)
Comment on phenotypes: Chediak-Higashi syndrome 214500Created: 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)
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 HypopigmentationCreated: 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 syndromeCreated: 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: ENST00000389794Created: 17 Apr 2018, 12:12 p.m.
Details
- Mode of Inheritance
- BIALLELIC, autosomal or pseudoautosomal
- Sources
-
- Expert Review Green
- Other
- NHS GMS
- North West GLH
- London North GLH
- IUIS Classification February 2018
- Victorian Clinical Genetics Services
- ESID Registry 20171117
- GRID V2.0
- GOSH PID v.8.0
- Phenotypes
-
- 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
- Tags
- OMIM
- 606897
- Clinvar variants
- Variants in LYST
- Penetrance
- None
- Publications
- Panels with this gene
-
- Inherited bleeding disorders
- Adult onset hereditary spastic paraplegia
- Fetal anomalies
- Hereditary neuropathy or pain disorder
- Childhood onset hereditary spastic paraplegia
- Ocular and oculo-cutaneous albinism
- Cytopenia - NOT Fanconi anaemia
- Rare genetic inflammatory skin disorders
- Hereditary neuropathy
- Adult onset dystonia, chorea or related movement disorder
- Primary immunodeficiency or monogenic inflammatory bowel disease
- Early onset or syndromic epilepsy
- Bleeding and platelet disorders
- DDG2P
- Infantile nystagmus
- Vici Syndrome and other autophagy disorders
- Optic neuropathy
- Intellectual disability
- Pigmentary skin disorders
- COVID-19 research
- Adult onset neurodegenerative disorder
- Parkinson Disease and Complex Parkinsonism
- Hereditary spastic paraplegia
- Albinism or congenital nystagmus
History Filter Activity
Entity classified by Genomics England curator
Eleanor Williams (Genomics England Curator)Gene: lyst has been classified as Green List (High Evidence).
Added New Source, Set publications, Status Update
Eleanor Williams (Genomics England Curator)Source Other was added to LYST. Publications for gene LYST were updated from 8896560; 9215679; 9215680; 10482950 to 9215679; 18043242; 8717042; 9215680; 10482950; 8896560; 26944273; 29939658 Rating Changed from Green List (high evidence) to Red List (low evidence)
Added New Source
Louise Daugherty (Genomics England Curator)Source NHS GMS was added to LYST.
Added New Source
Louise Daugherty (Genomics England Curator)Source North West GLH was added to LYST.
Added New Source
Louise Daugherty (Genomics England Curator)Source London North GLH was added to LYST.
Panel promoted to version 1.0
Louise Daugherty (Genomics England Curator)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.
Set penetrance
Louise Daugherty (Genomics England Curator)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
Added New Source
Louise Daugherty (Genomics England Curator)IUIS Classification February 2018 was added to LYST. Panel: Primary immunodeficiency disorders
Added New Source
Louise Daugherty (Genomics England Curator)Victorian Clinical Genetics Services was added to LYST. Panel: Primary immunodeficiency disorders
Entity classified by Genomics England curator
Louise Daugherty (Genomics England Curator)Gene: lyst has been classified as Green List (High Evidence).
Set Phenotypes
Louise Daugherty (Genomics England Curator)Phenotypes for LYST were set to Chediak-Higashi syndrome 214500; Chediak Higashi syndrome
Set publications
Sarah Leigh (Genomics England Curator)Publications for LYST were set to 8896560; 9215679; 9215680; 10482950
Set Phenotypes
Sarah Leigh (Genomics England Curator)Phenotypes for LYST were set to Chediak-Higashi syndrome 214500
Gene classified by Genomics England curator
Sarah Leigh (Genomics England Curator)This gene has been classified as Green List (High Evidence).
Set Phenotypes
Louise Daugherty (Genomics England Curator)Phenotypes for LYST were set to Chediak-Higashi syndrome
Added New Source
Louise Daugherty (Genomics England Curator)Expert Review Amber was added to LYST. Panel: Primary immunodeficiency disorders
Added New Source, Set penetrance
Louise Daugherty (Genomics England Curator)ESID Registry 20171117 was added to LYST. Panel: Primary immunodeficiency disorders Phenotypes for gene LYST were set to Chediak-Higashi syndrome, Chediak Higashi syndrome
Set penetrance
Louise Daugherty (Genomics England Curator)Phenotypes for gene LYST were set to Chediak-Higashi syndrome
Added New Source, Set penetrance
Louise Daugherty (Genomics England Curator)GRID V2.0 was added to LYST. Panel: Primary immunodeficiency disorders Phenotypes for gene LYST were set to Chediak-Higashi syndrome
Clear Sources
Louise Daugherty (Genomics England Curator)LYST Source: GOSH PID 20171168 was removed from gene: LYST
Added New Source
Louise Daugherty (Genomics England Curator)GOSH PID v.8.0 was added to LYST. Panel: Primary immunodeficiency disorders
Added New Source
Louise Daugherty (Genomics England Curator)LYST was added to Primary immunodeficiency disorders panel. Sources: GOSH PID 20171168
Created
Louise Daugherty (Genomics England Curator)LYST was created by Louise Daugherty