Hereditary spastic paraplegia - childhood onset

Gene: SLC33A1

Red List (low evidence)

SLC33A1 (solute carrier family 33 member 1)
EnsemblGeneIds (GRCh38): ENSG00000169359
EnsemblGeneIds (GRCh37): ENSG00000169359
OMIM: 603690, Gene2Phenotype
SLC33A1 is in 11 panels

3 reviews

Nick Beauchamp (Sheffield Diagnostic Genetics Service)

Red List (low evidence)

Adult and childhood onset; single family. No additional patients identified using Sheffield panel.
Created: 10 May 2019, 9:35 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Publications

Variants in this GENE are reported as part of current diagnostic practice

Louise Daugherty (Genomics England Curator)

I don't know

Amber gene with Green and Red GLH rating, Gene discussed in view of discrepant rating(s) from GLH(s). Red rating agreed at the GMS Neurology Specialist Test Group Webex on 17th May 2019.
Created: 21 May 2019, 4:50 p.m.
Rating and review submitted on behalf of James Polke (Neurogenetics Laboratory,Institute of Neurology, London), on behalf of London North GLH for GMS Neurology specialist test group.
Created: 9 May 2019, 4:54 p.m.
Amber rating on Hereditary spastic paraplegia panel 1.198


helen kingston (CMFT NHS Foundation Trust, Manchester)
5 Nov 2017 Submitted Green review.



Comment when marking as ready: Very clear association of autosomal recessive mutations with congenital cataracts, hearing loss, and neurodegeneration. Limited evidence currently for HSP
emma baple (Genomics England Curator), 10 May 2016


A mutation in this gene has been described in one chinese family affected by pure HSP, showing autosomal dominant inheritance with reduced penetrance. A subsequent screen of 220 pure HSP patients of mostly caucasian origin failed to identify mutations with this gene.
Arianna Tucci (Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square), 13 Jan 2016. Submitted Amber rating
Created: 2 May 2019, 4:50 p.m.

James Polke (Neurogenetics Laboratory, Institute of Neurology, London)

Green List (high evidence)

several unrelated families published with CCHLND, affected members of a large Chinese family with pure autosomal dominant spastic paraplegia-42 . In sheffield HSP panel
Created: 28 Apr 2019, 4:16 p.m.

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Phenotypes
Congenital cataracts, hearing loss, and neurodegeneration, 614482, AR; Spastic paraplegia 42, autosomal dominant 612539, AD

Details

Mode of Inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • Expert Review Red
  • Yorkshire and North East GLH
  • NHS GMS
  • London North GLH
  • Illumina TruGenome Clinical Sequencing Services
  • Expert list
  • UKGTN
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Congenital cataracts, hearing loss, and neurodegeneration, 614482, AR
  • Spastic paraplegia 42, autosomal dominant
OMIM
603690
Clinvar variants
Variants in SLC33A1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

21 May 2019, Gel status: 1

Added New Source, Status Update

Louise Daugherty (Genomics England Curator)

Source Expert Review Red was added to SLC33A1. Rating Changed from Amber List (moderate evidence) to Red List (low evidence)

13 May 2019, Gel status: 2

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: SLC33A1 were set to Lin et al. (2008)

13 May 2019, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source Yorkshire and North East GLH was added to SLC33A1.

3 May 2019, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: slc33a1 has been classified as Amber List (Moderate Evidence).

2 May 2019, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: slc33a1 has been classified as Red List (Low Evidence).

28 Apr 2019, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: SLC33A1 were changed from Spastic paraplegia 42, autosomal dominant, to Congenital cataracts, hearing loss, and neurodegeneration, 614482, AR; Spastic paraplegia 42, autosomal dominant

28 Apr 2019, Gel status: 3

Set mode of inheritance

Louise Daugherty (Genomics England Curator)

Mode of inheritance for gene: SLC33A1 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

28 Apr 2019, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: slc33a1 has been classified as Green List (High Evidence).

28 Apr 2019, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to SLC33A1.

28 Apr 2019, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to SLC33A1.

3 Apr 2019, Gel status: 1

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Added phenotypes Spastic paraplegia 42, autosomal dominant, for gene: SLC33A1

28 Jan 2019, Gel status: 1

Panel promoted to version 1.0

Louise Daugherty (Genomics England Curator)

Rebecca Foulger: Comment on list classification

19 Dec 2018, Gel status: 1

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

Sarah Leigh (Genomics England Curator)

gene: SLC33A1 was added gene: SLC33A1 was added to Hereditary spastic paraplegia - childhood onset. Sources: Radboud University Medical Center, Nijmegen,UKGTN,Expert list,Expert Review Red,Illumina TruGenome Clinical Sequencing Services Mode of inheritance for gene: SLC33A1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: SLC33A1 were set to Lin et al. (2008) Phenotypes for gene: SLC33A1 were set to Spastic paraplegia 42, autosomal dominant,