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Genetic epilepsy syndromes

Gene: PTPN23

Green List (high evidence)

PTPN23 (protein tyrosine phosphatase, non-receptor type 23)
EnsemblGeneIds (GRCh38): ENSG00000076201
EnsemblGeneIds (GRCh37): ENSG00000076201
OMIM: 606584, Gene2Phenotype
PTPN23 is in 3 panels

3 reviews

Rebecca Foulger (Genomics England curator)

I don't know

Review and rating collated by Tracy Lester (Oxford Medical Genetics Laboratories Oxford University Hospitals NHS Foundation Trust, 2019_02_06) on behalf of Wessex and West Midlands GLH for GMS Neurology specialist test group, for Clinical Indication R59 'Early onset or syndromic epilepsy'. Review contributors: John Taylor and Helen Lord. Suggested gene rating: Green.
Created: 6 Aug 2019, 8:38 p.m. | Last Modified: 6 Aug 2019, 8:38 p.m.
Panel Version: 1.189

Tracy Lester (Genetics laboratory, Oxford UK)

Green List (high evidence)

No OMIM entry re disease. HGMD Pro - 6 variants listed. Alzami et al 2015 - hom missense variant in a child with global dev delay, epilepsy and brain atrophy. Trujillano et al, hom missense variant in a proband with a similar phenotype. Sowada et al, 2017 - novel compound het variant in a non consang proband - similar clinical picture as before - nonsense and a missense. Also reviewing patient from Alzami et al. 3D structure suggests the missense variant would have an effect. Smigiel et al, 2018 - proband -non consang - similar phenotype - compound het (missense and a fs) - functional work support pathogenicity. Rare but all patients with disease do have epilepsy as part of there phentoype and structural/functional studies back this up so far.
Created: 6 Aug 2019, 8:31 p.m. | Last Modified: 6 Aug 2019, 8:31 p.m.
Panel Version: 1.188

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
epileptic encephalopathy

Publications

Sarah Leigh (Genomics England Curator)

Comment when marking as ready: Not associated with phenotype in OMIM or in Gen2Phen, at least 5 variants reported in 3 unrelated cases, together with functional studies and knock-out mouse model. PMID 25558065, first report of PTPN23 homozygous variant (NM_015466.2:c.3995G>T:p.R1332L) in third child of first cousin parents (older sibs died in infancy); 5 year old boy with developmental delay, cerebral palsy, seizure disorder and gastroesophageal reflux disease. PMID: 29899372 reports clinical phenotype of recessive PTPN23 variants ( c.1902C>G (p.(Asn634Lys)) and c.2974delC (p.(Leu992Tyrfs*168)) in a compound heterozygous case with pathogenicity substantiated by functional studies. PMID 29090338 c.3586C>T (p.Arg1196*) and c.1595C>T (p.Pro532Leu) in compound heterozygous case together with embryonic lethality in a PTPN23 knock-out mouse model.
Created: 31 Jul 2018, 11:02 a.m.
Comment on phenotypes: phenotype includes severe developmental delay, epilepsy, cortical blindness, hypomyelination and brain atrophy on MRI (PMID 29899372)
Created: 31 Jul 2018, 10:51 a.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Wessex and West Midlands GLH
  • NHS GMS
  • Expert Review Green
  • Victorian Clinical Genetics Services
Phenotypes
  • Rare severe autosomal-recessive developmental and epileptic encephalopathy
OMIM
606584
Clinvar variants
Variants in PTPN23
Penetrance
None
Publications
Panels with this gene

History Filter Activity

6 Aug 2019, Gel status: 3

Added New Source

Rebecca Foulger (Genomics England curator)

Source Wessex and West Midlands GLH was added to PTPN23.

6 Aug 2019, Gel status: 3

Added New Source

Rebecca Foulger (Genomics England curator)

Source NHS GMS was added to PTPN23.

11 Dec 2018, Gel status: 3

Panel promoted to version 1.0

Sarah Leigh (Genomics England Curator)

Sarah Leigh: Comment on phenotypes: phenoty

31 Jul 2018, Gel status: 3

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: ptpn23 has been classified as Green List (High Evidence).

31 Jul 2018, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: ptpn23 has been classified as Amber List (Moderate Evidence).

31 Jul 2018, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: PTPN23 were set to 25558065; 29899372; 29090338

31 Jul 2018, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: PTPN23 were set to 29899372; 29090338

31 Jul 2018, Gel status: 2

Set mode of inheritance

Sarah Leigh (Genomics England Curator)

Mode of inheritance for gene: PTPN23 was changed from to BIALLELIC, autosomal or pseudoautosomal

31 Jul 2018, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: PTPN23 were set to Rare severe autosomal-recessive developmental and epileptic encephalopathy

25 Jun 2018, Gel status: 2

Added New Source

Sarah Leigh (Genomics England Curator)

Expert Review Amber was added to PTPN23. Panel: Genetic Epilepsy Syndromes

25 Jun 2018, Gel status: 1

Added New Source

Sarah Leigh (Genomics England Curator)

PTPN23 was added to Genetic Epilepsy Syndromes panel. Sources: Victorian Clinical Genetics Services

25 Jun 2018, Gel status: 1

Created

Sarah Leigh (Genomics England Curator)

PTPN23 was created by Sarah Leigh