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Intellectual disability

Gene: PTPN4

Amber List (moderate evidence)

PTPN4 (protein tyrosine phosphatase, non-receptor type 4)
EnsemblGeneIds (GRCh38): ENSG00000088179
EnsemblGeneIds (GRCh37): ENSG00000088179
OMIM: 176878, Gene2Phenotype
PTPN4 is in 1 panel

2 reviews

Ivone Leong (Genomics England Curator)

Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. Based on the expert review, there is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Created: 28 Jul 2021, 2:31 p.m. | Last Modified: 28 Jul 2021, 2:31 p.m.
Panel Version: 3.1209
Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is not associated with a phenotype in OMIM or Gene2Phenotype. Based on the expert review, there is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Created: 28 Jul 2021, 2:31 p.m. | Last Modified: 28 Jul 2021, 2:31 p.m.
Panel Version: 3.1209

Zornitza Stark (Australian Genomics)

Green List (high evidence)

>3 unrelated probands and supportive mouse model
PMID: 17953619 - knockout mouse model has impaired motor learning and cerebellar synaptic plasticity
PMID: 25424712 - twins with a de novo whole gene deletion and a Rett-like neurodevelopmental disorder
PMID: 30238967 - mosaic de novo variant (p.Leu72Ser) identified in a child with developmental delay, autistic features, hypotonia, increased immunoglobulin E and dental problems. Also supporting mouse assays demonstrating loss of protein expression in dendritic spines
DOI: https://doi.org/10.1016/j.xhgg.2021.100033 - missense and truncating variants in six unrelated individuals with varying degrees of intellectual disability or developmental delay. 5 were able to undergo segregation analysis and found to be de novo.
Sources: Literature
Created: 10 May 2021, 10:26 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Intellectual disability

Publications

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

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Amber
Phenotypes
  • Intellectual disability, MONDO:0001071
Tags
Q3_21_rating
OMIM
176878
Clinvar variants
Variants in PTPN4
Penetrance
None
Publications
Panels with this gene

History Filter Activity

28 Jul 2021, Gel status: 2

Entity classified by Genomics England curator

Ivone Leong (Genomics England Curator)

Gene: ptpn4 has been classified as Amber List (Moderate Evidence).

28 Jul 2021, Gel status: 2

Entity classified by Genomics England curator

Ivone Leong (Genomics England Curator)

Gene: ptpn4 has been classified as Amber List (Moderate Evidence).

28 Jul 2021, Gel status: 0

Added Tag

Ivone Leong (Genomics England Curator)

Tag Q3_21_rating tag was added to gene: PTPN4.

27 Jul 2021, Gel status: 0

Set Phenotypes

Ivone Leong (Genomics England Curator)

Phenotypes for gene: PTPN4 were changed from Intellectual disability to Intellectual disability, MONDO:0001071

27 Jul 2021, Gel status: 0

Set publications

Ivone Leong (Genomics England Curator)

Publications for gene: PTPN4 were set to 17953619; 25424712; 30238967; DOI: https://doi.org/10.1016/j.xhgg.2021.100033

10 May 2021, Gel status: 0

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

Zornitza Stark (Australian Genomics)

gene: PTPN4 was added gene: PTPN4 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: PTPN4 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: PTPN4 were set to 17953619; 25424712; 30238967; DOI: https://doi.org/10.1016/j.xhgg.2021.100033 Phenotypes for gene: PTPN4 were set to Intellectual disability Review for gene: PTPN4 was set to GREEN gene: PTPN4 was marked as current diagnostic