0%
PTPN11c.1505C>TNot classified
Print report
Variant interpretation report

PTPN11 c.1505C>T, p.(Ser502Leu)

NM_002834.4:c.1505C>T NP_002825.3:p.(Ser502Leu) View identifiers
Classification
Not classified

Variant description:

No variant summary was recorded for this case.

Five-step scale from benign to pathogenic. Select a step to read what it means.

Not classified yet.Select a step to read what it means.

In plain language

Gene-level background from the recorded interpretation.

About PTPN11

No gene-level summary was recorded for this case.

LYFE Sciences is an AI system, and it can make mistakes. Criteria may be applied incorrectly, sources may be misread, and a confident-looking classification can still be wrong. Double-check every criterion and its underlying evidence before relying on any call.
01The reasoning

How it was classified

The recorded framework is ClinGen PTPN11 VCEP v1.0. The criteria and strengths shown below come from the saved assessment; this page does not recalculate the classification.

Recorded applied criteria

The applied criteria and their strengths are shown as assessed under the stated framework.

Pathogenic evidence criteria: 0 Benign evidence criteria: 0
Pathogenic criteria applied · 0

No pathogenic criterion marked as applied in the recorded assessment.

Benign criteria applied · 0

No benign criterion marked as applied in the recorded assessment.

Recorded classification: Not classified

In progress — classification not generated yet.

02The sources

Evidence at a glance

Evidence summaries and captured source records, where available. Missing entries should not be interpreted as negative findings.

gnomAD v4.1
gnomAD v2.1
Population frequency
0 / 1,614,128 alleles

gnomAD v4.1: 0 / 1,614,128 alleles. Recorded AF 0. Recorded homozygote count 0.

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

No listed criterion applied
gnomAD v4.1 ↗gnomAD v2.1 ↗gnomAD-Canada ↗
SpliceAI score
0.010 maximum delta

Recorded SpliceAI maximum delta score: 0.010. Refer to the recorded PP3/BP4 rationale for interpretation.

No listed criterion applied SpliceAI ↗
ClinVar submissions
11 reported laboratory submissions

11 Pathogenic. ClinVar API review status: criteria provided, multiple submitters, no conflicts.

Context only ClinVar ↗
Functional evidence
Statement recorded

In progress — evidence not uploaded yet.

No listed criterion applied OncoKB ↗
COSMIC
Cancer Hotspots
Somatic evidence
No matching record reported

This variant has not previously been reported in somatic cancers (COSMIC).

Cancer Hotspots

This variant lies in a statistically significant hotspot.

Context only
COSMIC ↗Cancer Hotspots ↗
For specialists

Technical detail

ACMG/AMP criteria under ClinGen PTPN11 VCEP v1.0, with the data and sources behind each one.

28 criteria with recorded statuses: 0 met · 0 not met · 28 not assessed · 0 not applicable. Open any row for the full reasoning, the rule and the evidence behind it.

Pathogenic
PVS1PS1PS2PS3PS4PM1PM2PM3PM4PM5PM6PP1PP2PP3PP4PP5
Benign
BA1BS1BS2BS3BS4BP1BP2BP3BP4BP5BP6BP7
Met Not met Not assessed Not applicable

Not assessed · 28 · no assessment recorded

PVS1 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PS1 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PS2 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PS3 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PS4 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PM1 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PM2 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PM3 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PM4 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PM5 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PM6 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PP1 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PP2 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PP3 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PP4 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

PP5 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BA1 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BS1 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BS2 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BS3 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BS4 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BP1 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BP2 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BP3 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BP4 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BP5 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BP6 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BP7 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

Identifiers

Gene
PTPN11
Transcript
NM_002834.4
Coding (HGVS c.)
NM_002834.4:c.1505C>T
Protein (HGVS p.)
NP_002825.3:p.(Ser502Leu)
GRCh38
chr12:112489081 C>T
GRCh37
chr12:112926885 C>T
ClinVar
40557, 13332

Gene diagram

Every interpreted variant in PTPN11, mapped onto the exon structure of NM_002834.4. Select a row to find it on the plot.

PTPN11NM_002834.4
Fetching transcript structure from UCSC…
gnomAD v4.1 0 / 1,614,128 alleles AF 0 · 0 homozygotes
gnomAD v2.1 Allele count data not recorded
gnomAD-Canada v1.0 0 / 0 alleles AF 0 · 0 homozygotes

By genetic ancestry

gnomAD v4.1

AF 0 · 0 / 1,614,128 alleles · 0 hom
No alternate alleles recorded in the displayed ancestry groups.

gnomAD-Canada

AF 0 · 0 / 0 alleles · 0 hom

Statements

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 0; MAF= 0.00000%, 0/1614128 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/75032 alleles, homozygotes = 0).

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

Open the gnomAD-Canada detail page →

SpliceAI and Pangolin

SpliceAI acceptor lossat -19 bp
0.000
SpliceAI acceptor gainat +140 bp
0.000
SpliceAI donor lossat +94 bp
0.000
SpliceAI donor gainat -3 bp
0.010
Pangolin splice lossmagnitude shown
-0.010
Pangolin splice gain
0.000

Other predictors

REVEL
0.976
BayesDel
0.542

How the predictions were used

PP3 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BP4 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

BP7 No criterion-specific rationale recorded. Details ▾Hide ▴

No further detail was recorded.

Statement

In silico

In progress — evidence not uploaded yet.

8 paper records listed. No publication is explicitly linked to an applied criterion in the recorded metadata. None of the listed paper records explicitly indicates that the variant is named.

Recorded publications

  • Functional analysis of PTPN11/SHP-2 mutants identified in Noonan syndrome and childhood leukemia.
    No paper-specific finding is recorded.
    PMID 15834506 ↗
  • PTPN11 mutations in Noonan syndrome type I: detection of recurrent mutations in exons 3 and 13.
    Maheshwari M et al. · 2002
    No paper-specific finding is recorded.
    PMID 12325025 ↗
  • Prognostic, therapeutic, and mechanistic implications of a mouse model of leukemia evoked by Shp2 (PTPN11) mutations.
    Mohi MG et al. · 2005
    No paper-specific finding is recorded.
    PMID 15710330 ↗
  • The mutational spectrum of PTPN11 in juvenile myelomonocytic leukemia and Noonan syndrome/myeloproliferative disease.
    Kratz CP et al. · 2005
    No paper-specific finding is recorded.
    PMID 15928039 ↗
  • Diversity and functional consequences of germline and somatic PTPN11 mutations in human disease.
    Tartaglia M et al. · 2006
    No paper-specific finding is recorded.
    PMID 16358218 ↗
  • PTPN11 gene analysis in 74 Brazilian patients with Noonan syndrome or Noonan-like phenotype.
    Bertola DR et al. · 2006
    No paper-specific finding is recorded.
    PMID 17020470 ↗
  • Mutations of FLT3, NRAS, KRAS, and PTPN11 are frequent and possibly mutually exclusive in high hyperdiploid childhood acute lymphoblastic leukemia.
    Paulsson K et al. · 2008
    No paper-specific finding is recorded.
    PMID 17910045 ↗
  • Loss-of-function mutations in PTPN11 cause metachondromatosis, but not Ollier disease or Maffucci syndrome.
    No paper-specific finding is recorded.
    PMID 21533187 ↗

Screenshots represent source records captured during evidence collection. Select one to view the recorded source content.

gnomAD v4.1 0 / 1,614,128 recorded alleles Open source ↗
gnomAD v2.1 Captured gnomAD v2.1 source record Open source ↗
SpliceAI Lookup Recorded maximum delta 0.010 Open source ↗
ClinVar 11 Pathogenic Open source ↗
COSMIC Captured COSMIC source record Open source ↗
Cancer hotspots Captured Cancer Hotspots source record Open source ↗
OncoKB Captured OncoKB source record Open source ↗
ClinGen CSpec Captured ClinGen CSpec source record Open source ↗

All source links

Statements for reports

The evidence statements recorded by the interpretation pipeline. They have not been reinterpreted by the page.

gnomAD v4.1

This variant is present in gnomAD v4.1 (AF= 0; MAF= 0.00000%, 0/1614128 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 0; MAF= 0.00000%, 0/75032 alleles, homozygotes = 0).

gnomAD v2.1

Absent from gnomAD v2.1.

gnomAD-Canada

Absent from gnomAD-Canada v1.0.

ClinVar

In progress — evidence not uploaded yet.

In silico

In progress — evidence not uploaded yet.

Functional

In progress — evidence not uploaded yet.

Somatic

In progress — evidence not uploaded yet.

Cancer Hotspots

This variant lies in a statistically significant hotspot.

Literature

In progress — evidence not uploaded yet.