GENE REFERENCE / HGNC:9644

PTPN11

protein tyrosine phosphatase non-receptor type 11

protein-coding gene12q24.13Gene information

What does this gene do?

The PTPN11 gene provides instructions for making a protein called SHP-2. This protein helps regulate the RAS/MAPK signaling pathway. This pathway is involved in several important cell functions, including the growth and division of cells (proliferation), the process by which cells mature to carry out specific functions (differentiation), cell movement (migration), and the self-destruction of cells (apoptosis). During embryonic development, the SHP-2 protein is critical in the development of the heart, blood cells, bones, and several other tissues.

The PTPN11 gene belongs to a class of genes known as oncogenes. When mutated, oncogenes have the potential to cause normal cells to become cancerous.

Source: MedlinePlus, National Library of Medicine. Source publication: 2023-04-24. Source review: 2016-06.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
Noonan syndromeMONDO:0018997 · Evaluated 2018-07-24	Autosomal dominant	DefinitiveRASopathy Gene Curation Expert Panel
Costello syndromeMONDO:0009026 · Evaluated 2018-05-31	Autosomal dominant	DisputedRASopathy Gene Curation Expert Panel
cardiofaciocutaneous syndromeMONDO:0015280 · Evaluated 2018-05-30	Autosomal dominant	DisputedRASopathy Gene Curation Expert Panel
Noonan syndrome with multiple lentiginesMONDO:0007893 · Evaluated 2018-07-25	Autosomal dominant	DefinitiveRASopathy Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 1,403
Submissions for variants in or overlapping this gene: 4,342
Submissions explicitly reporting this gene: 4,307
Alleles reported pathogenic / likely pathogenic: 209
VariationIDs with uncertain significance: 544
VariationIDs with conflicting classifications: 76

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about PTPN11?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 209 alleles in PTPN11 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in PTPN11.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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