Hereditary spastic paraplegia

Gene: LYST

Amber List (moderate evidence)

LYST (lysosomal trafficking regulator)
EnsemblGeneIds (GRCh38): ENSG00000143669
EnsemblGeneIds (GRCh37): ENSG00000143669
OMIM: 606897, Gene2Phenotype
LYST is in 23 panels

4 reviews

Louise Daugherty (Genomics England Curator)

I don't know

Gene to be reviewed again after the GMS Neurology specialist test group have reviewed and agreed rating of gene on the Hereditary spastic paraplegia - childhood onset panel on May 2019
Created: 3 May 2019, 8:36 a.m.

Rebecca Foulger (Genomics England curator)

Comment on publications: PMIDs:25519960 and 25519961 are in Japanese.
Created: 8 Jan 2019, 3:42 p.m.
Comment on list classification: Updated rating from Red to Amber. Gene added to panel by Chris Buxton (Bristol NHS) based on one family in PMID:24521565. In addition, progressive spastic paraparesis seen in affected siblings in PMID:26307451, and PMIDs 25519960 and 25519961 describe LYST as a potential HSP locus. Further cases required for a diagnostic rating.
Created: 8 Jan 2019, 3:42 p.m.
PMID:26307451 (Desai et al 2016) report 3 affected siblings with the late-onset form of CHS, and phenotypes including progressive spastic paraparesis.
Created: 8 Jan 2019, 3:37 p.m.
PMID:24521565 (Shimazaki et al 2014) include 2 patients in a Japanese family with parents who are first cousins. They detected a homozygous missense variant (c.4189T>G, p.F1397V) in the LYST gene. The patients had adult Chediak-Higashi syndrome (CHS) presenting spastic paraplegia with cerebellar ataxia and neuropathy.
Created: 8 Jan 2019, 3:37 p.m.

Sarah Leigh (Genomics England Curator)

Comment on list classification: This gene is awaiting curator evaluation and rating.
Created: 19 Dec 2018, 2:12 p.m.

Chris Buxton (North Bristol NHS Trust)

Shimazaki (2014, 24521565), homozygous LYST (c.4189T>G, p.F1397V).
Gene predominantly associated with Chediak-Higashi syndrome. one publication describing a HSP like phenotype.
Diagnostic on Sheffield HSP panel
Sources: Literature
Created: 28 Nov 2018, 9:20 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
spastic paraplegia

Publications

History Filter Activity

8 Jan 2019, Gel status: 2

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: LYST were changed from spastic paraplegia to spastic paraplegia; Chediak-Higashi syndrome, 214500

8 Jan 2019, Gel status: 2

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: LYST were set to 24521565

8 Jan 2019, Gel status: 2

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: lyst has been classified as Amber List (Moderate Evidence).

8 Jan 2019, Gel status: 1

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: lyst has been classified as Red List (Low Evidence).

19 Dec 2018, Gel status: 1

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: lyst has been classified as Red List (Low Evidence).

28 Nov 2018, Gel status: 0

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

Chris Buxton (North Bristol NHS Trust)

gene: LYST was added gene: LYST was added to Hereditary spastic paraplegia. Sources: Literature Mode of inheritance for gene: LYST was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: LYST were set to 24521565 Phenotypes for gene: LYST were set to spastic paraplegia Penetrance for gene: LYST were set to unknown