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  3. SPTLC2
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Hereditary neuropathy or pain disorder

Gene: SPTLC2

Green List (high evidence)
SPTLC2 (serine palmitoyltransferase long chain base subunit 2)
EnsemblGeneIds (GRCh38): ENSG00000100596
EnsemblGeneIds (GRCh37): ENSG00000100596
OMIM: 605713, Gene2Phenotype
SPTLC2 is in 13 panels

8 reviews

Natalie Forrester (SWGLH - Bristol Genetics)

Green List (high evidence)

Multiple C5s in Bristol. Also well established from looking at HGMD. PMID: 20920666 - first report showing mutations result in a partial to complete loss of SPT activity in vitro and in vivo
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 IC, 613640 ; Hereditary Sensory and Autonomic Neuropathy, Type IC

Publications

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

Created: 29 Apr 2019, 12:30 p.m.

Panel version: Imported from Hereditary neuropathy panel version 1.58

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.
Created: 29 Apr 2019, 9:26 a.m.

Panel version: Imported from Hereditary neuropathy panel version 1.80

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

Green List (high evidence)

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

Created: 29 Apr 2019, 9:20 a.m.

Panel version: Imported from Hereditary neuropathy panel version 1.52

Rita Horvath (Institute of Genetic Medicine, Newcastle University)

Green List (high evidence)

Created: 5 Nov 2017, 2:39 a.m.

Panel version: Imported from Hereditary neuropathy panel version 0

Thalia Antoniadi (West Midlands Regional Genetics Laboratory)

Green List (high evidence)

Created: 5 Nov 2017, 2:39 a.m.

Panel version: Imported from Hereditary neuropathy panel version 0

Alexander Rossor (UCL Institute of Neurology)

Green List (high evidence)

As above
Created: 9 Dec 2015, 8:48 a.m.

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

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

Created: 9 Dec 2015, 8:48 a.m.

Panel version: Imported from Hereditary neuropathy panel version 0

Ellen McDonagh (Genomics England Curator)

Comment on mode of pathogenicity: Missense variants reported in OMIM, which would come under tier 2.
Created: 10 May 2016, 11:15 a.m.
Comment on list classification: All four reviewers agree this should be green.
Created: 10 May 2016, 11:02 a.m.
"As above" refers to the comments for the SPTLC1 gene by Mary Reilly.
Created: 8 Dec 2015, 3:16 p.m.
Created: 8 Dec 2015, 3:16 p.m.

Panel version: Imported from Hereditary neuropathy panel version 0

Mary Reilly (Institute of Neurology)

Green List (high evidence)

As above
Created: 8 Dec 2015, 3:05 p.m.

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

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

Created: 8 Dec 2015, 3:05 p.m.

Panel version: Imported from Hereditary neuropathy panel version 0

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Radboud University Medical Center, Nijmegen
  • South West GLH
  • Expert Review Green
  • UKGTN
  • Emory Genetics Laboratory
  • Expert list
  • London North GLH
  • Illumina TruGenome Clinical Sequencing Services
  • NHS GMS
  • South West GLH
  • NHS GMS
  • London North GLH
Phenotypes
  • Hereditary Sensory and Autonomic Neuropathy, Type IC
  • Neuropathy, hereditary sensory and autonomic, type IC, 613640
OMIM
605713
Clinvar variants
Variants in SPTLC2
Penetrance
None
Publications
Mode of Pathogenicity
Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Panels with this gene

History Filter Activity

5 Dec 2019, Gel status: 3

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

Ellen McDonagh (Genomics England Curator)

gene: SPTLC2 was added gene: SPTLC2 was added to Hereditary neuropathy NOT PMP22 copy number. Sources: NHS GMS,Illumina TruGenome Clinical Sequencing Services,London North GLH,Expert list,Emory Genetics Laboratory,UKGTN,Expert Review Green,South West GLH,Radboud University Medical Center, Nijmegen Mode of inheritance for gene: SPTLC2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: SPTLC2 were set to 20920666 Phenotypes for gene: SPTLC2 were set to Hereditary Sensory and Autonomic Neuropathy, Type IC; Neuropathy, hereditary sensory and autonomic, type IC, 613640 Mode of pathogenicity for gene: SPTLC2 was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments