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PTPN11
Final classification
VUS
PTPN11 c.169C>A · p.Gln57Lys
PTPN11

NM_002834.4:c.169C>A (p.Gln57Lys) is a missense variant in PTPN11, a gene associated with autosomal dominant RASopathies.

Gene
PTPN11
Transcript
NM_002834.4
HGVS · transcript:coding
NM_002834.4:c.169C>A
Consequence
N/A
GRCh38
chr12:112450349 C>A
GRCh37
chr12:112888153 C>A
Basis ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTPN11 Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
ClinGen RASopathy Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for PTPN11 Version 2.3.0 v2.3.0 criteria-combination framework was evaluated deterministically with applied criteria: PM2 supporting, PP2 supporting, PP3 supporting; no rule matched the adjudicated criteria.
Classification rationale
PM2PP2PP3 VUS
PTPN11 c.169C>A

NM_002834.4:c.169C>A (p.Gln57Lys) is a missense variant in PTPN11, a gene associated with autosomal dominant RASopathies. The variant is absent from gnomAD v2.1 and v4.1 population databases, satisfying PM2 at Supporting strength under the RASopathy VCEP v2.3.0.1 REVEL in silico prediction score is 0.709, meeting the VCEP PP3 threshold of >=0.7 at Supporting strength.2 PTPN11 has a missense z-score well above 3.09 in gnomAD, satisfying PP2 at Supporting strength under the VCEP rule.3 The variant is absent from ClinVar with no prior classifications, and no publications describe this specific variant.4 PM1 is not applicable: position 57 (Gln57) is adjacent to but not within the VCEP-defined functional domain residues (AA 58-63 are the closest listed range).5 No functional studies have tested p.Gln57Lys in any VCEP-approved assay (SHP-2 Phosphatase Activity, MEK Activation, ERK Activation).6 No de novo, segregation, proband-count, or case-control data are available for this variant. Under the RASopathy VCEP v2.3.0 classification rules, three Supporting-level pathogenic criteria (PM2_Supporting, PP2, PP3) are met. No Strong, Very Strong, Moderate, or Stand-Alone criteria are met on either the pathogenic or benign side.7 The VCEP classification framework requires at minimum either (a) one Strong criterion with >=2 Supportive, or (b) one Moderate criterion with >=4 Supportive, or (c) >=2 Moderate criteria to reach Likely Pathogenic. None of these thresholds are met. No benign criteria are triggered.8 Final classification: Variant of Uncertain Significance (VUS).

PM2 + PP2 + PP3 VUS
2 revelcspec ↗
6 vcep_svi_rasopathy_vcep_v2_approved_functional_studies
Gene diagram · NM_002834.4 · variants mapped to exon structure
PTPN11 NM_002834.4
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 15 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
The variant is absent from gnomAD v2.1 and v4.1 population databases. Under the RASopathy VCEP v2.3.0, PM2 is applied at Supporting strength when the variant is absent from controls (gnomAD).
Absent from gnomAD v2.1 exomes (AC=0).Absent from gnomAD v4.1 exomes (AC=0).
PP2 supporting review Pathogenic
PTPN11 has a missense z-score well above 3.09 in gnomAD (v2.1: z=5.68; v4.1: z=7.03), satisfying the RASopathy VCEP v2.3.0 rule that PP2 applies at Supporting strength when the gnomAD missense z-score exceeds 3.09.
PTPN11 gnomAD missense z-score >> 3.09 threshold (v2.1 ~5.68v4.1 ~7.03).
PP3 supporting Pathogenic
REVEL score of 0.709 meets the RASopathy VCEP v2.3.0 threshold of >=0.7 for PP3 at Supporting strength. SpliceAI predicts no significant splice impact (max delta = 0.03), consistent with a missense mechanism.
REVEL score 0.709 >= 0.7 (VCEP threshold).SpliceAI max delta = 0.03 (no splice impact).
Assessed · not applied
Pathogenic
PS1 No previously established pathogenic variant at the same amino acid (Gln57) was identified in ClinVar or the literature.
PS2 No de novo occurrence with confirmed maternity and paternity was identified for this variant in any reviewed source.
PS3 The variant p.Gln57Lys has not been tested in any VCEP-approved functional assay (SHP-2 Phosphatase Activity, MEK Activation, or ERK Activation).
PS4 No proband or case-control data are available for this variant.
PM1 Under the RASopathy VCEP v2.3.0, PM1 is restricted to specific directly interacting residues between N-SH2 and PTPN domains: AA 4, 7-9, 58-63, 69-77, 247, 251, 255, 256, 258, 261, 265, 278-281, 284.
PM5 No likely pathogenic or pathogenic variant at the same codon (Gln57) was identified in ClinVar.
PM6 No assumed de novo occurrence (without confirmation of paternity and maternity) was identified for this variant in any reviewed source.
PP1 No co-segregation data are available for this variant.
Benign
BA1 The variant is absent from gnomAD (allele frequency = 0%).
BS1 The variant is absent from gnomAD.
BS2 No healthy adult individuals have been reported to carry this variant.
BS4 No segregation data are available to demonstrate lack of segregation in affected family members.
BP2 No evidence of an alternative molecular cause of RASopathy in the same gene or in trans/cis with a pathogenic variant.
BP4 REVEL score of 0.709 exceeds the RASopathy VCEP v2.3.0 BP4 threshold of <=0.3.
BP5 No alternative molecular cause of RASopathy in a different gene has been identified for any proband carrying this variant.
N/A · 10 PVS1 · PM3 · PM4 · PP4 · PP5 · BS3 · BP1 · BP3 · BP6 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
Absent from gnomAD v4.1.
v2.1
Absent from gnomAD v2.1.
🇨🇦 CA
Absent from gnomAD-Canada v1.0.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD v2.1
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
gnomAD Canada 🇨🇦
Absent · 0 / ?
0 hom
Not observed in any ancestry group.
ClinVar screenshot
ClinVar
This variant is absent from ClinVar.
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.03). REVEL score = 0.709. BayesDel score = 0.16136.
Functional / OncoKB screenshot
Functional Unknown Oncogenic Effect
OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. PTPN11, a protein tyrosine phosphatase, is altered in various solid and hematologic malignancies.
OncoKB ↗
COSMIC screenshot
COSMIC
Cancer hotspots screenshot
Cancer hotspots
Somatic evidence Not in COSMIC / hotspots
COSMIC
This variant does not lie in a statistically significant hotspot. This variant has not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
9Sources
CSpec VCEP
ClinVar
gnomAD v2.1
gnomAD v4.1
gnomAD-Canada
SpliceAI
OncoKB
COSMIC
Cancer hotspots