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Relevance to Autism

Chmielewska et al., 2021 reported six unrelated individuals with missense or protein-truncating variants in the PTPN4 gene who exhibited varying degrees of intellectual disability or developmental delay; two of these individuals presented with autism spectrum disorder, and the missense variant identified in one of these individuals with ASD (p.Gly239Arg in patient 1 in this report) was shown experimentally to result in failure of PTPN4 to localize to the dendritic spines of transfected rat hippocampal neurons, in contrast to WT PTPN4. Mutations in PTPN4 had previously been identifed in monozygotic twins presenting with a Rett syndrome-like phenotype characterized by developmental delay, seizures, and stereotypic hand movements (Williamson et al., 2015), as well as in a child presenting with developmental delay, autistic features, and upper limb stereotypies (Szczauba et al., 2018).

Molecular Function

The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This protein contains a C-terminal PTP domain and an N-terminal domain homologous to the band 4.1 superfamily of cytoskeletal-associated proteins. This PTP has been shown to interact with glutamate receptor delta 2 and epsilon subunits, and is thought to play a role in signalling downstream of the glutamate receptors through tyrosine dephosphorylation.

External Links

        

References

Type
Title
Type of Disorder
Associated Disorders
Author, Year
Primary
PTPN4 germline variants result in aberrant neurodevelopment and growth
DD, ID
ASD, ADHD, epilepsy/seizures
Support
ASD
DD, ID
Support
Integrating de novo and inherited variants in 42
ASD
Support
Neurodevelopmental phenotype caused by a de novo PTPN4 single nucleotide variant disrupting protein localization in neuronal dendritic spines
DD
Autistic features, stereotypy
Support
Deletion of protein tyrosine phosphatase, non-receptor type 4 (PTPN4) in twins with a Rett syndrome-like phenotype
DD, epilepsy/seizures
Stereotypy

Rare

Variant ID
Variant Type
Allele Change
Residue Change
Inheritance Pattern
Inheritance Association
Family Type
Author, Year
 GEN1293R001 
 missense_variant 
 c.715G>A 
 p.Gly239Arg 
 De novo 
  
 Multiplex 
 GEN1293R002 
 missense_variant 
 c.191T>G 
 p.Leu64Trp 
 De novo 
  
  
 GEN1293R003 
 frameshift_variant 
 c.393_396del 
 p.Gln132ThrfsTer17 
 De novo 
  
  
 GEN1293R004 
 missense_variant 
 c.2171T>C 
 p.Ile724Thr 
 De novo 
  
  
 GEN1293R005 
 stop_gained 
 c.2512C>T 
 p.Arg838Ter 
 Unknown 
  
  
 GEN1293R006 
 missense_variant 
 c.1738G>T 
 p.Asp580Tyr 
 De novo 
  
 Multiplex 
 GEN1293R007 
 copy_number_loss 
  
  
 De novo 
  
 Multiplex (monozygotic twins) 
 GEN1293R008 
 missense_variant 
 c.215T>C 
 p.Leu72Ser 
 De novo 
  
  
 GEN1293R009 
 stop_gained 
 c.1171C>T 
 p.Arg391Ter 
 De novo 
  
  
 GEN1293R010 
 missense_variant 
 c.2619A>T 
 p.Glu873Asp 
 Familial 
 Maternal 
 Simplex 

Common

No Common Variants Available
Chromosome
CNV Locus
CNV Type
# of studies
Animal Model
2
Duplication
 1
 
2
Duplication
 1
 
2
Duplication
 2
 
2
Deletion
 1
 
2
Deletion-Duplication
 14
 

No Animal Model Data Available

 

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