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_002834.5(PTPN11):c.209A>G (p.Lys70Arg)

CA261568

44603 (ClinVar)

Gene: PTPN11
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 3b04afbf-2784-4140-8597-2108c5253464
Approved on: 2020-06-25
Published on: 2020-06-25

HGVS expressions

NM_002834.5:c.209A>G
NM_002834.5(PTPN11):c.209A>G (p.Lys70Arg)
NM_002834.3:c.209A>G
NM_080601.1:c.209A>G
NM_001330437.1:c.209A>G
NM_002834.4:c.209A>G
NM_080601.2:c.209A>G
NM_001330437.2:c.209A>G
NM_001374625.1:c.206A>G
NM_080601.3:c.209A>G
ENST00000351677.6:c.209A>G
ENST00000392597.5:c.209A>G
ENST00000635625.1:n.209A>G
NC_000012.12:g.112450389A>G
CM000674.2:g.112450389A>G
NC_000012.11:g.112888193A>G
CM000674.1:g.112888193A>G
NC_000012.10:g.111372576A>G
NG_007459.1:g.36658A>G
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Pathogenic

Met criteria codes 6
PM2 PM6 PM1 PS4 PP2 PP1

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.2019A>G (p.Lys70Arg) variant in PTPN11 was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). It has been identified in at least 6 probands with Noonan syndrome (PS4; SCV000061296.6; PMID: 29084544).One case was described as an unconfirmed de novo occurrence (PM6; PMID: 29084544). It has been reported to segregate with clinical features of a RASopathy in at least 3 family members (PP1; SCV000061296.6). 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). Finally, PTPN11 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, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS4, PM6, PM1, PM2, PP1, PP2.
Met criteria codes
PM2
Absent from gnomAD
PM1
Defined hotspot between N-SH2 and PTPN domains
PS4
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
PP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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