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.184T>G (p.Tyr62Asp)

CA234749

13329 (ClinVar)

Gene: PTPN11
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: f5564d77-9990-4f45-94f7-6ebb47bd39a9

HGVS expressions

NM_002834.4:c.184T>G
NM_002834.4(PTPN11):c.184T>G (p.Tyr62Asp)
NM_002834.3:c.184T>G
NM_080601.1:c.184T>G
NM_001330437.1:c.184T>G
NM_080601.2:c.184T>G
NM_001330437.2:c.184T>G
NM_001374625.1:c.181T>G
NM_002834.5:c.184T>G
NM_080601.3:c.184T>G
ENST00000351677.6:c.184T>G
ENST00000392597.5:c.184T>G
ENST00000635625.1:n.184T>G
NC_000012.12:g.112450364T>G
CM000674.2:g.112450364T>G
NC_000012.11:g.112888168T>G
CM000674.1:g.112888168T>G
NC_000012.10:g.111372551T>G
NG_007459.1:g.36633T>G

Pathogenic

Met criteria codes 7
PS3 PS4 PP2 PP3 PM1 PM2 PM6

Evidence Links 6

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.184T>G (p.Tyr62Asp) variant in PTPN11 is absent from gnomAD (PM2). This variant has been observed in multiple individuals with Noonan syndrome (PS4; SCV000659042.4, PMIDs: 26817465, 19352411, 17020470, 12325025, 11992261, 19077116, 17339163). It has also been reported in the literature as an unconfirmed de novo occurrence in a patient with clinical features of a RASopathy (PM6; PMID: 12325025). In vitro functional studies provide some evidence that the p.Tyr62Asp variant may impact protein function (PS3; PMID: 22711529). Furthermore, the variant is in a location that has been defined by the ClinGen RASopathy Expert Panel to be a mutational hotspot or domain of PTPN11 (PM1; PMID: 29493581). Computational prediction tools and conservation analysis suggest the variant may impact the protein (PP3). Additionally, the p.Tyr62Asp variant is located in the PTPN11 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). In summary, the p.Tyr62Asp variant in PTPN11 meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID: 29493581): PM2, PS4, PM6, PS3, PM1, PP3, PP2.
Met criteria codes
PS3
PS4
6 individuals with NS identified (LMM internal data)

PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL .9
PM1
Located in the N-SH2 domain, a well established functional domain.
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2020-02-14
Published on: 2020-02-18
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