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Hereditary neuropathy
Gene: SPTLC2

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

9 reviews

Dmitrijs Rots (Children's Clinical University Hospital)

Green List (high evidence)

Also associated with ALS now PMID: 38041679 and 38041684 via gain of function mechanism
Created: 24 Aug 2024, 1:44 p.m. | Last Modified: 24 Aug 2024, 1:44 p.m.

Panel Version: 1.489

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
ALS

Publications

PMID: 38041679
38041684

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

Created: 24 Aug 2024, 1:44 p.m.
Last Modified: 24 Aug 2024, 1:44 p.m.
Panel version: 1.489

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

20920666

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

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

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: 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: 1.52

Rita Horvath (Institute of Genetic Medicine, Newcastle University)

Green List (high evidence)

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

Panel version: 0

Thalia Antoniadi (West Midlands Regional Genetics Laboratory)

Green List (high evidence)

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

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: 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: 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: 0

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

20920666

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