Variant
PTPN11 I56T
NM_002834.5(PTPN11):c.167T>C (p.Ile56Thr)
- p.Ile56Thr
- p.I56T
- rs1052382672
- ClinVar classification
- Likely pathogenic
- Review status
- 3 stars out of 4reviewed by expert panel
- Last evaluated
- 10 May 2019
- Expert panel
- ClinGen RASopathy Variant Curation Expert Panel
Data current to ClinVar release 2026-10-12 · Dante Labs data release 2026.10.16-c6eea6bfFacts last changed 16 October 2026
Reference genomeGRCh38hg38
Positions on gene and variant pages follow this choice, in this browser.
Summary
I56T is a missense variant in PTPN11: it changes a single amino acid in the protein the gene encodes. ClinVar classifies it as likely pathogenic for Noonan Syndrome and Noonan-Related Syndromes (reviewed by expert panel).
ClinVar classifications
| Condition | Classification | Review status | Submissions | Last evaluated |
|---|---|---|---|---|
| Noonan Syndrome and Noonan-Related SyndromesClinVar VCV000477669 (opens in a new tab) | Likely pathogenic | 3 stars out of 4reviewed by expert panel | 1 submission | 10 May 2019 |
Classifications as ClinVar records them in release 2026-10-12. ClinVar updates them as evidence is reviewed.
Molecular details
| Gene | PTPN11 |
|---|---|
| Transcript | NM_002834.5MANE Select |
| Coding DNA change (HGVS c.) | c.167T>C |
| Protein change (HGVS p.) | p.Ile56Thrp.I56T |
| Predicted consequence | Missensemissense_variant (opens in a new tab) |
| Predicted impact | Moderate |
| Position (GRCh38) | chr12:112450347 T>C |
| Position (GRCh37) | chr12:112888151 T>C |
| dbSNP ID | rs1052382672 (opens in a new tab) |
| ClinVar Variation ID | VCV000477669 (opens in a new tab) |
| ClinVar Allele ID | 462420 |
| ClinGen Allele Registry ID | CA243707917 (opens in a new tab) |
| ClinVar name | NM_002834.5(PTPN11):c.167T>C (p.Ile56Thr) |
PTPN11 I56T in other databases
Reports that look at this variant (2)
These Genome Test condition reports include I56T among the variants they look at.
| Report | Conditions | Inheritance |
|---|---|---|
| Hypertrophic Cardiomyopathy | Hypertrophic Cardiomyopathy | Autosomal dominant |
| Noonan Syndrome | Noonan Syndrome and Noonan-Related Syndromes |
Other variants in PTPN11
- E139DPathogenic3 stars out of 4
- I56VPathogenic3 stars out of 4
- M504VPathogenic3 stars out of 4
- N308DPathogenic3 stars out of 4
- Q510PPathogenic3 stars out of 4
- T468MPathogenic3 stars out of 4
- Y63CPathogenic3 stars out of 4
Limitations
This page describes publicly available information about a genetic variant. It is not a diagnosis, and it says nothing about whether you or anyone else carries this variant.
Classifications come from ClinVar and change as new evidence is reviewed. A classification here may differ from the one in ClinVar today, or from the one a laboratory reports.
Whole genome sequencing with short reads can miss or miscall some variants, particularly in repeated or highly similar stretches of DNA and in large insertions, deletions or rearrangements.
If you have questions about a variant in your own results or in your family, talk to a genetic counsellor or your doctor.
Sources & credits
- Classifications from ClinVar (release 2026-10-12), National Center for Biotechnology Information.
- Condition terms from the Mondo Disease Ontology (release 2026-10-06), used under CC BY 4.0.
- Gene symbols and names from the HUGO Gene Nomenclature Committee (release 2026-10-16).
- Allele identifiers from the ClinGen Allele Registry (release 2026-10-16-c4908f54).
- Reference SNP identifiers from dbSNP (release b157), National Center for Biotechnology Information.
- Gene–disease links from the Gene Curation Coalition, GenCC (release 2026-10-16).
- Difficult regions from the Genome in a Bottle Consortium (release v3.6).
- Transcripts from MANE (release v1.5), NCBI and EMBL-EBI.
- Predicted consequences from mehari (release 0.11.0), with transcript models from cdot.
- Built from Dante Labs data release 2026.10.16-c6eea6bf of 16 October 2026.
Cite this page
Dante Labs. (16 October 2026). PTPN11 I56T (c.167T>C, rs1052382672) (Version 2026.10.16-c6eea6bf). Retrieved 16 October 2026, from https://dantelabs.com/genes/ptpn11/variants/i56t
Dante Labs. PTPN11 I56T (c.167T>C, rs1052382672) [Internet]. Version 2026.10.16-c6eea6bf. 16 October 2026 [cited 16 October 2026]. Available from: https://dantelabs.com/genes/ptpn11/variants/i56t
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