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Intellectual disability

Gene: LYST

Red List (low evidence)

LYST (lysosomal trafficking regulator)
EnsemblGeneIds (GRCh38): ENSG00000143669
EnsemblGeneIds (GRCh37): ENSG00000143669
OMIM: 606897, Gene2Phenotype
LYST is in 24 panels

4 reviews

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

Associated with relevant phenotypes (which include intellectual disability) 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: 23 Jul 2018, 1:26 p.m.

Helen Brittain (Genomics England Curator)

Comment when marking as ready: ID is not a common feature in Chediak-Higashi syndrome. There is a reported case, however both parents had intellectual disability raising the strong possibility of an alternative cause.
Created: 21 Dec 2017, 11:34 a.m.
Comment on list classification: ID is not a common feature in Chediak-Higashi syndrome. There is a reported case, however both parents had intellectual disability raising the strong possibility of an alternative cause.
Created: 21 Dec 2017, 11:33 a.m.

BRIDGE consortium (NIHRBR-RD)

Green List (high evidence)

This is a pertinent gene from the NIHR BioResource - Rare Diseases Study (NIHRBR-RD) BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene is on the SPEED_NEURO_20170705 gene list. Evidences used for SPEED NEURO gene list: in_ddg2p_20141118_conf;in_ddg2p_20141118_conf;in_ddg2p_201507;in_ddg2p_201507_conf;in_ddg2p_2_4_2017;in_ddg2p_2_4_2017_conf;in_movement_disorder_list . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 7:20 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; manju_list; neuro_20160418_strict; Loss of function. This is a pertinent gene from the BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene comes from the SPEED_NEURO_v3.0_20170404 gene list. The following experts from the BRIDGE consortium NIHRBR-RD contributed to this panel: - Professor F. Lucy Raymond, Cambridge Institute for Medical Research, University of Cambridge - Manju Kurian, Paediatric neurologist, Great Ormond Street Hosptial - Keren Carss, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Alba Sanchis-Juan, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Marie Erwood NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Louise Daugherty, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust
Created: 19 Jul 2017, 12:47 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

  • 25529582
  • Personal communication with NIHRBRRD BRIDGE SPEED

Louise Daugherty (Genomics England Curator)

Red List (low evidence)

After internal clinical review it was agreed that although this gene is rated Green the Genetic Epilepsy Syndromes panel and there is a cognitive deterioration, after a period of normal development, this does no fit well within the scope of the ID panel so should be rated red
Created: 25 Jul 2018, 8:45 a.m.
Recent Green review of this gene in the EE panel.Hediak-Higashi syndrome (CHS) is a rare autosomal recessive disease characterized by varying degrees of oculocutaneous albinism, recurrent infections, and a mild bleeding tendency, with late neurologic dysfunction. Cognitive deficits are often noted in childhood. Most patients develop neurological features by early adulthood as the disease progresses including ataxia, tremor, absent deep-tendon reflexes, and peripheral neuropathy- this phenotype is more associated to movement disorder than ID, suggest keep gene Red
Created: 24 Jul 2018, 11:56 a.m.
Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to assess inclusion and pertinence to this panel.
Created: 20 Jul 2017, 12:22 p.m.

History Filter Activity

29 Sep 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to LYST.

24 Jul 2018, Gel status: 1

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: LYST were set to Gene2Phenotype confirmed gene with ID HPO; Chediak-Higashi syndrome, 214500

12 Mar 2018, Gel status: 1

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

5 Jan 2018, Gel status: 1

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

20 Jul 2017, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

20 Jul 2017, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

19 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

LYST was created by BRIDGE

19 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

LYST was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene