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Gene

PTPN11

protein tyrosine phosphatase non-receptor type 11

Summary

Cytogenetic location
12q24.13
Coordinates
Chromosome 12: 112,418,947–112,509,918 (GRCh38)
Exons
16 exons across 91 kb
Protein
593 amino acids
Inheritance
Autosomal dominant
Also known as
BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2
Previous symbols
NS1
MANE Select transcript
ENST00000351677.7NM_002834.5
Locus type
gene with protein product
  • Very high
  • Confident
  • Low
  • Very low

Reference genomeGRCh38

Positions on gene and variant pages follow this choice, in this browser.

Curated reports relevant to this gene

  • Noonan Syndrome

    • Autosomal dominant

      Noonan Syndrome (NS) is characterized by short stature, typical facial dysmorphism and congenital heart defects.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong
      What knowing changes

      Cardiac surveillance, developmental support, growth hormone therapy, genetic counseling, MEK inhibitor trials

    • Noonan Syndrome and Noonan-Related Syndromes

      A group of RAS pathway conditions, including Noonan, Costello, cardiofaciocutaneous and Legius syndromes, with variable heart defects, short stature and distinctive facial features.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong
      What knowing changes

      Knowing about it supports heart, growth and developmental assessment.

Broader groupings

  • Hypertrophic Cardiomyopathy

    • Autosomal dominant

      One of 62 genes linked to it

      A condition in which the myocardium is hypertrophied without an obvious cause. The hypertrophy is generally asymmetric and may be associated with obstruction of the ventricular outflow tract.

      • ClinGen rates the link definitive
      • 6 GenCC submitters rate it definitive or strong
      What knowing changes

      Beta-blockers, non-dihydropyridine calcium channel blockers, activity restriction, genetic counseling

Inheritance

Autosomal dominant
One changed copy, from either parent, is enough. A parent who has one passes it on to each child with a one-in-two chance.

How PTPN11 is laid out

  • Coding sequence
  • Untranslated region
  • Intron
  • Direction of transcription
  • Known disease-causing sites
  • Stretches short reads find hard
  • Variants with a page
Chromosome 12, with a bracket where PTPN11 sits. PTPN11 and 9 genes near it on chromosome 12, from 111,964,433 to 112,964,432.Chromosome 1212q24.13p13.33p13.32p13.31p13.2p13.1p12.3p12.2p12.1p11.23p11.22p11.21p11.1q11q12q13.11q13.12q13.13q13.2q13.3q14.1q14.2q14.3q15q21.1q21.2q21.31q21.32q21.33q22q23.1q23.2q23.3q24.11q24.12q24.13q24.21q24.22q24.23q24.31q24.32q24.33112 Mb112.2 Mb112.4 Mb112.6 Mb112.8 MbTMEM116: 111,893,714–112,014,271, reverse strandTMEM116ERP29: 112,012,815–112,026,066, forward strandERP29NAA25: 112,026,689–112,109,434, reverse strandNAA25TRAFD1: 112,125,514–112,153,610, forward strandTRAFD1HECTD4: 112,160,188–112,382,443, reverse strandHECTD4RPL6: 112,403,955–112,418,844, reverse strandRPL6PTPN11: 112,418,947–112,509,918, forward strandPTPN11RPH3A: 112,570,380–112,898,881, forward strandRPH3AOAS1: 112,905,856–112,933,219, forward strandOAS1OAS3: 112,938,051–112,976,460, forward strandOAS3Diagram of PTPN11: 16 exons on the forward strand of chromosome 12Exon 1: 4 known disease-causing sitesExon 2: 3 known disease-causing sitesExon 3: 36 known disease-causing sitesExon 4: 5 known disease-causing sitesExon 5: 3 known disease-causing sitesExon 6: 4 known disease-causing sitesExon 7: 18 known disease-causing sitesExon 8: 7 known disease-causing sitesExon 9: 5 known disease-causing sitesExon 10: 3 known disease-causing sitesExon 11: 4 known disease-causing sitesExon 12: 7 known disease-causing sitesExon 13: 21 known disease-causing sitesExon 14: 1 known disease-causing siteExon 1: 112,418,947–112,419,125, 179 basesExon 2: 112,446,276–112,446,398, 123 basesExon 3: 112,450,318–112,450,512, 195 bases. 3 variants with a page in exon 3. List themExon 4: 112,453,195–112,453,387, 193 bases. 1 variant with a page in exon 4. List themExon 5: 112,454,564–112,454,680, 117 basesExon 6: 112,455,950–112,456,063, 114 basesExon 7: 112,472,944–112,473,040, 97 basesExon 8: 112,477,651–112,477,730, 80 bases. 1 variant with a page in exon 8. List themExon 9: 112,477,857–112,478,015, 159 basesExon 10: 112,482,074–112,482,205, 132 basesExon 11: 112,486,475–112,486,629, 155 basesExon 12: 112,488,443–112,488,510, 68 bases. 1 variant with a page in exon 12. List themExon 13: 112,489,024–112,489,175, 152 bases. 2 variants with a page in exon 13. List themExon 14: 112,502,144–112,502,256, 113 basesExon 15: 112,504,695–112,504,796, 102 basesExon 16: 112,505,825–112,509,918, 4,094 bases12468101214165′3′

Exons of the gene's MANE Select transcript (release v1.5), from NCBI and EMBL-EBI, on the GRCh38 reference genome.

Chromosome bands from UCSC's GRCh38 ideogram (2022-10-29).

Nearby genes from Ensembl release 116, on GRCh38.

Exons make up 6.1 kb of the gene's 91 kb; 1,782 of those bases code for the protein.

How a genome test reads PTPN11

127

positions in PTPN11 where ClinVar classes a change as pathogenic or likely pathogenic

1 of them (0.8%) falls in a region short reads find hard.

  • Low mappability (1 site)Regions where 100 bp or 250 bp reads cannot be placed uniquely.

A whole genome covers all 91 kb of PTPN11, introns included, not only the 6.1 kb of exons.

Variants with a page (8)

The PTPN11 variants with a page here, most review stars first. Each page describes ClinVar's public record of the variant, never a result.

VariantHGVS c.Exon or intronPosition (GRCh38)ClinVar classificationReview status
E139Dc.417G>CExon 4112,453,279Pathogenic3 stars out of 4 reviewed by expert panel
I56Tc.167T>CExon 3112,450,347Likely pathogenic3 stars out of 4 reviewed by expert panel
I56Vc.166A>GExon 3112,450,346Pathogenic3 stars out of 4 reviewed by expert panel
M504Vc.1510A>GExon 13112,489,086Pathogenic3 stars out of 4 reviewed by expert panel
N308Dc.922A>GExon 8112,477,719Pathogenic3 stars out of 4 reviewed by expert panel
Q510Pc.1529A>CExon 13112,489,105Pathogenic3 stars out of 4 reviewed by expert panel
T468Mc.1403C>TExon 12112,488,466Pathogenic3 stars out of 4 reviewed by expert panel
Y63Cc.188A>GExon 3112,450,368Pathogenic3 stars out of 4 reviewed by expert panel

Where this comes from

  • HGNC: the gene's symbol, name, other symbols and location.
  • MANE Select v1.5, from NCBI and EMBL-EBI: the transcript, its exons and coding sequence.
  • GenCC and ClinGen, released 2026-10-16: which conditions the gene is linked to, and how strongly.
  • The ACMG secondary findings list, SF v3.2.
  • ClinVar and the GIAB stratifications: known disease-causing sites, and the regions short reads find hard.
  • The Human Phenotype Ontology, release 2026-09-01: the traits linked to the gene. Find out more at hpo.jax.org.
  • Data release 2026.10.16-c6eea6bf.

Cite this page

APA

Dante Labs. (n.d.). PTPN11 gene: protein tyrosine phosphatase non-receptor type 11. Retrieved 17 October 2026, from https://dantelabs.com/genes/ptpn11

Vancouver

Dante Labs. PTPN11 gene: protein tyrosine phosphatase non-receptor type 11 [Internet]. [cited 17 October 2026]. Available from: https://dantelabs.com/genes/ptpn11

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