Genes in panel

Hereditary neuropathy

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 11 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

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)

Thalia Antoniadi (West Midlands Regional Genetics Laboratory)

Green List (high evidence)

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

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.

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

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 IC
  • Neuropathy, hereditary sensory and autonomic, type IC, 613640
  • Neuropathy, hereditary sensory and autonomic, type IC, 613640
  • Hereditary Sensory and Autonomic Neuropathy, Type IC
OMIM
605713
Clinvar variants
Variants in SPTLC2
Penetrance
Complete
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

29 Apr 2019, Gel status: 4

Set Phenotypes, Set publications

Louise Daugherty (Genomics England Curator)

Added phenotypes Neuropathy, hereditary sensory and autonomic, type IC, 613640; Hereditary Sensory and Autonomic Neuropathy, Type IC for gene: SPTLC2 Publications for gene SPTLC2 were changed from to 20920666

29 Apr 2019, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Source South West GLH was added to SPTLC2.

29 Apr 2019, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Source NHS GMS was added to SPTLC2.

29 Apr 2019, Gel status: 3

Added New Source, Status Update

Louise Daugherty (Genomics England Curator)

Source London North GLH was added to SPTLC2. Rating Changed from Green List (high evidence) to Green List (high evidence)

8 Jul 2016, Gel status: 4

Gene classified by Genomics England curator

Richard Scott (Genomics England Curator)

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

10 May 2016, Gel status: 4

Set mode of pathogenicity

Ellen McDonagh (Genomics England Curator)

Mode of pathogenicity for SPTLC2 was changed to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments

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 SPTLC2 was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

20 Jul 2015, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC2 was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

20 Jul 2015, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC2 was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

20 Jul 2015, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC2 was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

20 Jul 2015, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC2 was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

20 Jul 2015, Gel status: 4

Set Mode of Inheritance

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene SPTLC2 was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

20 Jul 2015, Gel status: 4

Added New Source

Ellen McDonagh (Genomics England Curator)

SPTLC2 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 SPTLC2 was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

20 Jul 2015, Gel status: 3

Added New Source

Ellen McDonagh (Genomics England Curator)

SPTLC2 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 SPTLC2 was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

20 Jul 2015, Gel status: 2

Added New Source

Ellen McDonagh (Genomics England Curator)

SPTLC2 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 SPTLC2 was changed to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

20 Jul 2015, Gel status: 2

Added New Source

Ellen McDonagh (Genomics England Curator)

SPTLC2 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)

SPTLC2 was added to Charcot-Marie-Tooth diseasepanel. Sources: Radboud University Medical Center, Nijmegen,Illumina TruGenome Clinical Sequencing Services,Expert list,UKGTN,Emory Genetics Laboratory