PTPN11protein tyrosine phosphatase, non-receptor type 11
Autism Reports / Total Reports
9 / 29Rare Variants / Common Variants
50 / 0Aliases
PTPN11, BPTP3, CFC, MGC14433, NS1, PTP-1D, PTP2C, SH-PTP2, SH-PTP3, SHP2Associated Syndromes
Noonan syndrome, Noonan syndrome 1Chromosome Band
12q24.13Associated Disorders
DD/NDD, ID, EP, EPS, ASDRelevance to Autism
This gene has been associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with Noonan syndrome (Tartaglia et al., 2001).
Molecular Function
The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. This PTP contains two tandem Src homology-2 domains, which function as phospho-tyrosine binding domains and mediate the interaction of this PTP with its substrates. This PTP is widely expressed in most tissues and plays a regulatory role in various cell signaling events that are important for a diversity of cell functions, such as mitogenic activation, metabolic control, transcription regulation, and cell migration. Mutations in this gene are a cause of Noonan syndrome as well as acute myeloid leukemia.
External Links
SFARI Genomic Platforms
Reports related to PTPN11 (29 Reports)
# | Type | Title | Author, Year | Autism Report | Associated Disorders |
---|---|---|---|---|---|
1 | Primary | Mutations in PTPN11, encoding the protein tyrosine phosphatase SHP-2, cause Noonan syndrome | Tartaglia M , et al. (2001) | No | ASD |
2 | Recent Recommendation | Autism traits in the RASopathies | Adviento B , et al. (2013) | No | Autistic features |
3 | Recent Recommendation | Behavioral profile in RASopathies | Alfieri P , et al. (2014) | No | Autistic features |
4 | Support | The contribution of de novo coding mutations to autism spectrum disorder | Iossifov I et al. (2014) | Yes | - |
5 | Support | Large-scale discovery of novel genetic causes of developmental disorders | Deciphering Developmental Disorders Study (2014) | No | ASD, DD |
6 | Support | Excess of rare, inherited truncating mutations in autism | Krumm N , et al. (2015) | Yes | - |
7 | Recent Recommendation | De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies | Homsy J , et al. (2016) | No | DD, learning disabilities |
8 | Support | High diagnostic yield of syndromic intellectual disability by targeted next-generation sequencing | Martnez F , et al. (2016) | No | ID |
9 | Support | Clinical exome sequencing: results from 2819 samples reflecting 1000 families | Trujillano D , et al. (2016) | No | - |
10 | Support | Hotspots of missense mutation identify neurodevelopmental disorder genes and functional domains | Geisheker MR , et al. (2017) | Yes | - |
11 | Support | Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands | Jin SC , et al. (2017) | No | Neurodevelopmental disorders (NDD) |
12 | Support | Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder | Takata A , et al. (2018) | Yes | - |
13 | Support | PTPN11 Gain-of-Function Mutations Affect the Developing Human Brain, Memory, and Attention | Johnson EM , et al. (2018) | No | - |
14 | Support | Elucidation of the phenotypic spectrum and genetic landscape in primary and secondary microcephaly | Boonsawat P , et al. (2019) | No | DD, epilepsy/seizures |
15 | Support | Variant recurrence in neurodevelopmental disorders: the use of publicly available genomic data identifies clinically relevant pathogenic missense variants | Lecoquierre F , et al. (2019) | No | - |
16 | Support | Comprehensive Analysis of Rare Variants of 101 Autism-Linked Genes in a Hungarian Cohort of Autism Spectrum Disorder Patients | Balicza P , et al. (2019) | Yes | - |
17 | Support | - | Brunet T et al. (2021) | No | Epilepsy/seizures, autistic features |
18 | Support | - | Valentino F et al. (2021) | No | DD |
19 | Support | - | Rosenthal SB et al. (2021) | Yes | - |
20 | Support | - | Pode-Shakked B et al. (2021) | No | - |
21 | Support | - | Brea-Fernández AJ et al. (2022) | No | - |
22 | Support | - | Leite AJDC et al. (2022) | No | - |
23 | Support | - | Zhou X et al. (2022) | Yes | - |
24 | Support | - | Rai B et al. (2023) | No | - |
25 | Support | - | Tuncay IO et al. (2023) | Yes | - |
26 | Support | - | Sanchis-Juan A et al. (2023) | No | - |
27 | Support | - | Erica Rosina et al. (2024) | No | - |
28 | Support | - | Axel Schmidt et al. (2024) | No | ASD |
29 | Support | - | Karen Lob et al. () | Yes | ADHD, DD |
Rare Variants (50)
Status | Allele Change | Residue Change | Variant Type | Inheritance Pattern | Parental Transmission | Family Type | PubMed ID | Author, Year |
---|---|---|---|---|---|---|---|---|
c.9G>A | p.Ser3%3D | synonymous_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
c.182A>G | p.Asp61Gly | missense_variant | - | - | - | 11704759 | Tartaglia M , et al. (2001) | |
c.188A>G | p.Tyr63Cys | missense_variant | - | - | - | 11704759 | Tartaglia M , et al. (2001) | |
c.215C>G | p.Ala72Gly | missense_variant | - | - | - | 11704759 | Tartaglia M , et al. (2001) | |
c.228G>C | p.Glu76Asp | missense_variant | - | - | - | 11704759 | Tartaglia M , et al. (2001) | |
c.598A>T | p.Asn200Tyr | missense_variant | Unknown | - | - | 39136901 | Karen Lob et al. () | |
c.781C>T | p.Leu261Phe | missense_variant | Unknown | - | - | 39136901 | Karen Lob et al. () | |
c.844A>G | p.Ile282Val | missense_variant | - | - | - | 11704759 | Tartaglia M , et al. (2001) | |
c.922A>G | p.Asn308Asp | missense_variant | - | - | - | 11704759 | Tartaglia M , et al. (2001) | |
c.577C>G | p.Leu193Val | missense_variant | De novo | - | - | 35982159 | Zhou X et al. (2022) | |
c.184T>G | p.Tyr62Asp | missense_variant | De novo | - | - | 28991257 | Jin SC , et al. (2017) | |
c.1510A>G | p.Met504Val | missense_variant | - | - | - | 11704759 | Tartaglia M , et al. (2001) | |
c.221T>G | p.Leu74Trp | missense_variant | De novo | - | - | 26785492 | Homsy J , et al. (2016) | |
c.1517C>T | p.Ser506Leu | missense_variant | De novo | - | - | 28991257 | Jin SC , et al. (2017) | |
c.802G>T | p.Gly268Cys | missense_variant | De novo | - | - | 26785492 | Homsy J , et al. (2016) | |
c.922A>G | p.Asn308Asp | missense_variant | De novo | - | - | 26785492 | Homsy J , et al. (2016) | |
c.1520G>A | p.Gly507Glu | missense_variant | De novo | - | - | 26785492 | Homsy J , et al. (2016) | |
c.182A>G | p.Asp61Gly | missense_variant | De novo | - | - | 27620904 | Martnez F , et al. (2016) | |
c.854T>C | p.Phe285Ser | missense_variant | De novo | - | - | 35390071 | Leite AJDC et al. (2022) | |
c.1471C>A | p.Pro491Thr | missense_variant | De novo | - | - | 34356170 | Valentino F et al. (2021) | |
c.794G>A | p.Arg265Gln | missense_variant | Unknown | - | - | 39039281 | Axel Schmidt et al. (2024) | |
c.922A>G | p.Asn308Asp | missense_variant | De novo | - | - | 39039281 | Axel Schmidt et al. (2024) | |
c.1271C>T | p.Pro424Leu | missense_variant | De novo | - | - | 39039281 | Axel Schmidt et al. (2024) | |
c.854T>C | p.Phe285Ser | missense_variant | De novo | - | - | 27848944 | Trujillano D , et al. (2016) | |
c.1529A>G | p.Gln510Arg | missense_variant | De novo | - | Simplex | 35982159 | Zhou X et al. (2022) | |
c.166A>G | p.Ile56Val | missense_variant | De novo | - | Unknown | 33619735 | Brunet T et al. (2021) | |
c.1611+374C>T | - | intron_variant | Familial | Both parents | - | 37492102 | Tuncay IO et al. (2023) | |
c.1472C>A | p.Pro491His | missense_variant | Unknown | - | - | 28628100 | Geisheker MR , et al. (2017) | |
c.1492C>T | p.Arg498Trp | missense_variant | Unknown | - | - | 28628100 | Geisheker MR , et al. (2017) | |
c.1496C>T | p.Ser499Phe | missense_variant | Unknown | - | - | 28628100 | Geisheker MR , et al. (2017) | |
c.1546A>G | p.Met516Val | missense_variant | Unknown | - | - | 28628100 | Geisheker MR , et al. (2017) | |
c.1520G>A | p.Gly507Glu | missense_variant | De novo | - | Simplex | 25961944 | Krumm N , et al. (2015) | |
c.1510A>G | p.Met504Val | missense_variant | De novo | - | Unknown | 33619735 | Brunet T et al. (2021) | |
c.417G>C | p.Glu139Asp | missense_variant | De novo | - | Multiplex | 33619735 | Brunet T et al. (2021) | |
c.1403C>T | p.Thr468Met | missense_variant | De novo | - | Simplex | 29346770 | Takata A , et al. (2018) | |
c.1502G>A | p.Arg501Lys | stop_gained | Unknown | Not maternal | - | 31134136 | Balicza P , et al. (2019) | |
c.923A>G | p.Asn308Ser | missense_variant | De novo | - | Simplex | 30842647 | Boonsawat P , et al. (2019) | |
c.328G>A | p.Glu110Lys | missense_variant | De novo | - | Simplex | 38041506 | Erica Rosina et al. (2024) | |
c.1391G>C | p.Ser464Thr | missense_variant | De novo | - | Simplex | 38041506 | Erica Rosina et al. (2024) | |
c.214G>T | p.Ala72Ser | missense_variant | Familial | - | Multiplex | 11704759 | Tartaglia M , et al. (2001) | |
c.923A>G | p.Asn308Ser | missense_variant | De novo | - | Simplex | 34580403 | Pode-Shakked B et al. (2021) | |
c.417G>C | p.Glu139Asp | missense_variant | Unknown | - | Simplex | 37541188 | Sanchis-Juan A et al. (2023) | |
c.1507G>C | p.Gly503Arg | missense_variant | De novo | - | - | 35322241 | Brea-Fernández AJ et al. (2022) | |
c.1230del | p.Leu411SerfsTer65 | intron_variant | De novo | - | Simplex | 25363768 | Iossifov I et al. (2014) | |
c.236A>G | p.Gln79Arg | missense_variant | Familial | Paternal | Multiplex | 11704759 | Tartaglia M , et al. (2001) | |
c.1508G>A | p.Gly503Glu | missense_variant | Familial | Paternal | Multiplex | 28628100 | Geisheker MR , et al. (2017) | |
c.184T>G | p.Tyr62Asp | missense_variant | De novo | - | Simplex | 25533962 | Deciphering Developmental Disorders Study (2014) | |
c.1508G>A | p.Gly503Glu | missense_variant | Familial | Maternal | Multi-generational | 31036916 | Lecoquierre F , et al. (2019) | |
c.1507G>A | p.Gly503Arg | missense_variant | De novo | - | Multiplex | 25533962 | Deciphering Developmental Disorders Study (2014) | |
c.1546_1547insCTATCTATA | p.Tyr515_Met516insThrIleTyr | inframe_insertion | De novo | - | - | 39039281 | Axel Schmidt et al. (2024) |
Common Variants
No common variants reported.
SFARI Gene score
High Confidence, Syndromic
Score Delta: Score remained at 1S
criteria met
See SFARI Gene'scoring criteriaWe considered a rigorous statistical comparison between cases and controls, yielding genome-wide statistical significance, with independent replication, to be the strongest possible evidence for a gene. These criteria were relaxed slightly for category 2.
The syndromic category includes mutations that are associated with a substantial degree of increased risk and consistently linked to additional characteristics not required for an ASD diagnosis. If there is independent evidence implicating a gene in idiopathic ASD, it will be listed as "#S" (e.g., 2S, 3S, etc.). If there is no such independent evidence, the gene will be listed simply as "S."
1/1/2021
Score remained at 1
Description
This gene is associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with patients with Noonan syndrome (PMID 11704759). The prevalence of autistic traits in patients with Noonan syndrome has been quantified using standard assessment tools (PMIDs 24101678, 24458522). A de novo missense variant in the PTPN11 gene was identified in an ASD proband from the Simons Simplex Collection; no de novo SNVs in this gene were observed in unaffected SSC siblings (P=0.05) (PMID 25961944). The proteins encoded by PTPN11 and the high-confidence ASD gene MET interact with each other (PMID 8662733).
10/1/2019
Decreased from 4S to 1
New Scoring Scheme
Description
This gene is associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with patients with Noonan syndrome (PMID 11704759). The prevalence of autistic traits in patients with Noonan syndrome has been quantified using standard assessment tools (PMIDs 24101678, 24458522). A de novo missense variant in the PTPN11 gene was identified in an ASD proband from the Simons Simplex Collection; no de novo SNVs in this gene were observed in unaffected SSC siblings (P=0.05) (PMID 25961944). The proteins encoded by PTPN11 and the high-confidence ASD gene MET interact with each other (PMID 8662733).
Reports Added
[New Scoring Scheme]7/1/2019
Decreased from 4S to 4S
Description
This gene is associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with patients with Noonan syndrome (PMID 11704759). The prevalence of autistic traits in patients with Noonan syndrome has been quantified using standard assessment tools (PMIDs 24101678, 24458522). A de novo missense variant in the PTPN11 gene was identified in an ASD proband from the Simons Simplex Collection; no de novo SNVs in this gene were observed in unaffected SSC siblings (P=0.05) (PMID 25961944). The proteins encoded by PTPN11 and the high-confidence ASD gene MET interact with each other (PMID 8662733).
Reports Added
[Variantrecurrence in neurodevelopmental disorders: the use of publicly available genomic data identifies clinically relevant pathogenic missense v...2019] [Comprehensive Analysis of Rare Variants of 101 Autism-Linked Genes in a Hungarian Cohort of Autism Spectrum Disorder Patients.2019]4/1/2019
Decreased from 4S to 4S
Description
This gene is associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with patients with Noonan syndrome (PMID 11704759). The prevalence of autistic traits in patients with Noonan syndrome has been quantified using standard assessment tools (PMIDs 24101678, 24458522). A de novo missense variant in the PTPN11 gene was identified in an ASD proband from the Simons Simplex Collection; no de novo SNVs in this gene were observed in unaffected SSC siblings (P=0.05) (PMID 25961944). The proteins encoded by PTPN11 and the high-confidence ASD gene MET interact with each other (PMID 8662733).
7/1/2018
Decreased from 4S to 4S
Description
This gene is associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with patients with Noonan syndrome (PMID 11704759). The prevalence of autistic traits in patients with Noonan syndrome has been quantified using standard assessment tools (PMIDs 24101678, 24458522). A de novo missense variant in the PTPN11 gene was identified in an ASD proband from the Simons Simplex Collection; no de novo SNVs in this gene were observed in unaffected SSC siblings (P=0.05) (PMID 25961944). The proteins encoded by PTPN11 and the high-confidence ASD gene MET interact with each other (PMID 8662733).
10/1/2017
Decreased from 4S to 4S
Description
This gene is associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with patients with Noonan syndrome (PMID 11704759). The prevalence of autistic traits in patients with Noonan syndrome has been quantified using standard assessment tools (PMIDs 24101678, 24458522). A de novo missense variant in the PTPN11 gene was identified in an ASD proband from the Simons Simplex Collection; no de novo SNVs in this gene were observed in unaffected SSC siblings (P=0.05) (PMID 25961944). The proteins encoded by PTPN11 and the high-confidence ASD gene MET interact with each other (PMID 8662733).
7/1/2017
Decreased from 4S to 4S
Description
This gene is associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with patients with Noonan syndrome (PMID 11704759). The prevalence of autistic traits in patients with Noonan syndrome has been quantified using standard assessment tools (PMIDs 24101678, 24458522). A de novo missense variant in the PTPN11 gene was identified in an ASD proband from the Simons Simplex Collection; no de novo SNVs in this gene were observed in unaffected SSC siblings (P=0.05) (PMID 25961944). The proteins encoded by PTPN11 and the high-confidence ASD gene MET interact with each other (PMID 8662733).
10/1/2016
Decreased from 4S to 4S
Description
This gene is associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with patients with Noonan syndrome (PMID 11704759). The prevalence of autistic traits in patients with Noonan syndrome has been quantified using standard assessment tools (PMIDs 24101678, 24458522). A de novo missense variant in the PTPN11 gene was identified in an ASD proband from the Simons Simplex Collection; no de novo SNVs in this gene were observed in unaffected SSC siblings (P=0.05) (PMID 25961944). The proteins encoded by PTPN11 and the high-confidence ASD gene MET interact with each other (PMID 8662733).
1/1/2016
Decreased from 4S to 4S
Description
This gene is associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with patients with Noonan syndrome (PMID 11704759). The prevalence of autistic traits in patients with Noonan syndrome has been quantified using standard assessment tools (PMIDs 24101678, 24458522). A de novo missense variant in the PTPN11 gene was identified in an ASD proband from the Simons Simplex Collection; no de novo SNVs in this gene were observed in unaffected SSC siblings (P=0.05) (PMID 25961944). The proteins encoded by PTPN11 and the high-confidence ASD gene MET interact with each other (PMID 8662733).
Reports Added
[Large-scale discovery of novel genetic causes of developmental disorders.2014] [Autism traits in the RASopathies.2013] [Behavioral profile in RASopathies.2014] [Mutations in PTPN11, encoding the protein tyrosine phosphatase SHP-2, cause Noonan syndrome.2001] [Excess of rare, inherited truncating mutations in autism.2015] [The contribution of de novo coding mutations to autism spectrum disorder2014] [De novo mutations in congenital heart disease with neurodevelopmental and other congenital anomalies.2016]7/1/2015
Decreased from 5 to 4S
Description
This gene is associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with patients with Noonan syndrome (PMID 11704759). The prevalence of autistic traits in patients with Noonan syndrome has been quantified using standard assessment tools (PMIDs 24101678, 24458522). A de novo missense variant in the PTPN11 gene was identified in an ASD proband from the Simons Simplex Collection; no de novo SNVs in this gene were observed in unaffected SSC siblings (P=0.05) (PMID 25961944). The proteins encoded by PTPN11 and the high-confidence ASD gene MET interact with each other (PMID 8662733).
4/1/2015
Decreased from 5 to 5
Description
This gene has been associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with Noonan syndrome (PMID 11704759).
1/1/2015
Decreased from 5 to 5
Description
This gene has been associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with Noonan syndrome (PMID 11704759).
7/1/2014
Increased from No data to 5
Description
This gene has been associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with Noonan syndrome (PMID 11704759).
4/1/2014
Increased from No data to 5
Description
This gene has been associated with syndromic autism, where a subpopulation of individuals with a given syndrome develop autism. In particular, rare mutations of the PTPN11 gene have been identified with Noonan syndrome (PMID 11704759).
Krishnan Probability Score
Score 0.45429159814388
Ranking 10178/25841 scored genes
[Show Scoring Methodology]
ExAC Score
Score 0.99987723087868
Ranking 711/18225 scored genes
[Show Scoring Methodology]
Sanders TADA Score
Score 0.74337448425131
Ranking 1491/18665 scored genes
[Show Scoring Methodology]
Zhang D Score
Score 0.009701573082835
Ranking 8368/20870 scored genes
[Show Scoring Methodology]
Interactome
- Protein Binding
- DNA Binding
- RNA Binding
- Protein Modification
- Direct Regulation
- ASD-Linked Genes
Interaction Table
Interactor Symbol | Interactor Name | Interactor Organism | Interactor Type | Entrez ID | Uniprot ID |
---|---|---|---|---|---|
C-MET | Hepatocyte growth factor receptor | Human | Protein Binding | 4233 | P08581 |
GPX7 | Glutathione peroxidase 7 | Human | Protein Binding | 2882 | Q96SL4 |
LUM | Lumican | Human | Protein Binding | 4060 | P51884 |
PDCD1 | Programmed cell death protein 1 | Human | Protein Binding | 5133 | Q15116 |
TCEAL1 | Transcription elongation factor A protein-like 1 | Human | Protein Binding | 9338 | Q15170-2 |
TMEM220 | Transmembrane protein 220 | Human | Protein Binding | 388335 | Q6QAJ8-2 |