The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_002834.4(PTPN11):c.1529A>C (p.Gln510Pro)

CA256758

13344 (ClinVar)

Gene: PTPN11
Condition: Noonan syndrome with multiple lentigines
Inheritance Mode: Autosomal dominant inheritance
UUID: 74aa9bfb-79b2-4d78-8440-29866a548c82
Approved on: 2017-04-03
Published on: 2018-12-10

HGVS expressions

NM_002834.4:c.1529A>C
NM_002834.4(PTPN11):c.1529A>C (p.Gln510Pro)
NM_002834.3:c.1529A>C
NM_001330437.1:c.1541A>C
ENST00000351677.6:c.1529A>C
ENST00000635625.1:n.1541A>C
ENST00000635652.1:n.542A>C
NC_000012.12:g.112489105A>C
CM000674.2:g.112489105A>C
NC_000012.11:g.112926909A>C
CM000674.1:g.112926909A>C
NC_000012.10:g.111411292A>C
NG_007459.1:g.75374A>C
More

Pathogenic

Met criteria codes 6
PP1_Moderate PM2 PP3 PP2 PS2_Very Strong PS4_Supporting

Evidence Links 2

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.1529A>C (p.Gln510Pro) variant in PTPN11 has been reported as a confirmed de novo occurrence in at least 2 patients with clinical features of a RASopathy (PS2_VeryStrong; Partners LMM, GeneDx, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data, APHP-Robert Debré Hospital; SCV000057459.14; SCV000200027.4; SCV000265844.1;. PMID 15520399, 20578946). The p.Gln510Pro variant in PTPN11 has been reported in the literature to segregate with clinical features of a RASopathy in at least 4 family members (PP1_Moderate; APHP-Robert Debré Hospital: GTR Lab ID: 28338). The variant has also been identified in at least 2 independent occurrences in patients with clinical features of a RASopathy (PS4_Supporting; Partners LMM, GeneDx, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data, APHP-Robert Debré Hospital; SCV000057459.14; SCV000200027.4; SCV000265844.1;. PMID 15520399, 20578946). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is in PTPN11, which has been defined by the ClinGen RASopathy Expert Panel as a gene with low rate of benign missense with missense variants commonly being pathogenic (PP2; PMID 29493581). Computational prediction tools and conservation analysis suggest that the p.Gln510Pro variant may impact the protein (PP3). In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. ACMG/AMP criteria applied: PS2_VeryStrong, PP1_Moderate, PM2, PP2, PP3, PS4_Supporting.
Met criteria codes
PP1_Moderate
The p.Gln510Pro variant in PTPN11 has been reported in the literature to segregate with clinical features of a RASopathy in at least 4 family members (PP1_Moderate; APHP-Robert Debré Hospital: GTR Lab ID: 28338).
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2_Very Strong
The c.1529A>C (p.Gln510Pro) variant in PTPN11 has been reported as a confirmed de novo occurrence in at least 2 patients with clinical features of a RASopathy (PS2_VeryStrong; Partners LMM, GeneDx, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data, APHP-Robert Debré Hospital; SCV000057459.14; SCV000200027.4; SCV000265844.1;. PMID 15520399, 20578946).

PS4_Supporting
The variant has also been identified in at least 2 independent occurrences in patients with clinical features of a RASopathy (PS4_Supporting; Partners LMM, GeneDx, Institute of Human Genetics, Otto von Guericke University Magdeburg internal data, APHP-Robert Debré Hospital; SCV000057459.14; SCV000200027.4; SCV000265844.1;. PMID 15520399, 20578946).
Curation History
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