Genes in panel

Hereditary neuropathy

Gene: SPTLC1

Green List (high evidence)

SPTLC1 (serine palmitoyltransferase long chain base subunit 1)
EnsemblGeneIds (GRCh38): ENSG00000090054
EnsemblGeneIds (GRCh37): ENSG00000090054
OMIM: 605712, Gene2Phenotype
SPTLC1 is in 9 panels

8 reviews

Natalie Forrester (SWGLH - Bristol Genetics)

Green List (high evidence)

2 variants in 3 different probands with sensory neuropathy in Bristol. PMID: 20097765 - showed that the pathological mechanism in HSAN1 is the accumulation of neurotoxic metabolites rather than the reduced de novo sphingolipid synthesis i.e. stated that gain of function mechanism. PMID: 16216550 - heterozygous SPTLC1 and SPTLC2 knock-out mice, which have a significantly reduced SPT activity, do not develop neuropathic symptoms
Created: 29 Apr 2019, 12:30 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
Neuropathy, hereditary sensory and autonomic, type IA, 162400 ; Hereditary Sensory and Autonomic Neuropathy, Type II ; Neuropathy, hereditary sensory and autonomic, type IA, 162400

Publications

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

Louise Daugherty (Genomics England Curator)

I don't know

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, 5 p.m.
Review and rating submitted by Natalie Forrester (SWGLH - Bristol Genetics) on behalf of South West GLH for GMS Neurology specialist test group.
Created: 29 Apr 2019, 12:53 p.m.

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

Green List (high evidence)

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

Rita Horvath (Institute of Genetic Medicine, Newcastle University)

Green List (high evidence)

Mode of pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype -please provide details in the comments

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

Thalia Antoniadi (West Midlands Regional Genetics Laboratory)

Green List (high evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Ellen McDonagh (Genomics England Curator)

Comment on mode of inheritance: Changed due to feedback from QC team.
Created: 13 Mar 2017, 5:01 p.m.
This gene is in the Charcot Marie Tooth Disease section in the UCLH National Hospital for Neurology and Neurosurgery & Institute of Neurology (NHNN) Neurogenetics genetic testing manual, for testing of Hereditary Sensory and Autonomic Neuropathy.
Created: 10 Jun 2016, 1:20 p.m.
Comment on list classification: 4 reviewers agreeing.
Created: 10 May 2016, 10:58 a.m.

Alexander Rossor (UCL Institute of Neurology)

Green List (high evidence)

Disease due to toxic deoxysphingolipids
Created: 9 Dec 2015, 8:48 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Mode of pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype -please provide details in the comments

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

Mary Reilly (Institute of Neurology)

Green List (high evidence)

Disease due to toxic deoxysphingolipids
Created: 8 Dec 2015, 3:05 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Mode of pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype -please provide details in the comments

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

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • South West GLH
  • NHS GMS
  • London North GLH
  • Expert Review Green
  • Emory Genetics Laboratory
  • UKGTN
  • Expert list
  • Illumina TruGenome Clinical Sequencing Services
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Hereditary Sensory and Autonomic Neuropathy, Type II
  • Neuropathy, hereditary sensory and autonomic, type IA, 162400
  • Hereditary Sensory and Autonomic Neuropathy, Type II
  • Neuropathy, hereditary sensory and autonomic, type IA, 162400
OMIM
605712
Clinvar variants
Variants in SPTLC1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

29 Apr 2019, Gel status: 4

Set Phenotypes, Set publications

Louise Daugherty (Genomics England Curator)

Added phenotypes Hereditary Sensory and Autonomic Neuropathy, Type II; Neuropathy, hereditary sensory and autonomic, type IA, 162400 for gene: SPTLC1 Publications for gene SPTLC1 were changed from to 16216550; 20097765

29 Apr 2019, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Source South West GLH was added to SPTLC1.

29 Apr 2019, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to SPTLC1.

29 Apr 2019, Gel status: 3

Added New Source, Status Update

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to SPTLC1. Rating Changed from Green List (high evidence) to Green List (high evidence)

13 Mar 2017, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Mode of inheritance for SPTLC1 was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

10 May 2016, Gel status: 4

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

10 May 2016, Gel status: 4

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

20 Jul 2015, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC1 was changed to BIALLELIC, autosomal or pseudoautosomal

20 Jul 2015, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC1 was changed to BIALLELIC, autosomal or pseudoautosomal

20 Jul 2015, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC1 was changed to BIALLELIC, autosomal or pseudoautosomal

20 Jul 2015, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC1 was changed to BIALLELIC, autosomal or pseudoautosomal

20 Jul 2015, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC1 was changed to BIALLELIC, autosomal or pseudoautosomal

20 Jul 2015, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC1 was changed to BIALLELIC, autosomal or pseudoautosomal

20 Jul 2015, Gel status: 4

Added New Source

Ellen McDonagh (Genomics England Curator)

SPTLC1 was added to Charcot-Marie-Tooth diseasepanel. Sources: Radboud University Medical Center, Nijmegen,Illumina TruGenome Clinical Sequencing Services,Expert list,UKGTN,Emory Genetics Laboratory

20 Jul 2015, Gel status: 3

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC1 was changed to BIALLELIC, autosomal or pseudoautosomal

20 Jul 2015, Gel status: 3

Added New Source

Ellen McDonagh (Genomics England Curator)

SPTLC1 was added to Charcot-Marie-Tooth diseasepanel. Sources: Radboud University Medical Center, Nijmegen,Illumina TruGenome Clinical Sequencing Services,Expert list,UKGTN,Emory Genetics Laboratory

20 Jul 2015, Gel status: 2

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC1 was changed to BIALLELIC, autosomal or pseudoautosomal

20 Jul 2015, Gel status: 2

Added New Source

Ellen McDonagh (Genomics England Curator)

SPTLC1 was added to Charcot-Marie-Tooth diseasepanel. Sources: Radboud University Medical Center, Nijmegen,Illumina TruGenome Clinical Sequencing Services,Expert list,UKGTN,Emory Genetics Laboratory

20 Jul 2015, Gel status: 2

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC1 was changed to BIALLELIC, autosomal or pseudoautosomal

20 Jul 2015, Gel status: 2

Added New Source

Ellen McDonagh (Genomics England Curator)

SPTLC1 was added to Charcot-Marie-Tooth diseasepanel. Sources: Radboud University Medical Center, Nijmegen,Illumina TruGenome Clinical Sequencing Services,Expert list,UKGTN,Emory Genetics Laboratory

20 Jul 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

SPTLC1 was added to Charcot-Marie-Tooth diseasepanel. Sources: Radboud University Medical Center, Nijmegen,Illumina TruGenome Clinical Sequencing Services,Expert list,UKGTN,Emory Genetics Laboratory