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.922A>G (p.Asn308Asp)

CA220158

13326 (ClinVar)

Gene: PTPN11
Condition: Noonan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: 6525f07c-2ebf-4229-9447-62d126ad46cd
Approved on: 2017-04-03
Published on: 2018-12-10

HGVS expressions

NM_002834.4:c.922A>G
NM_002834.4(PTPN11):c.922A>G (p.Asn308Asp)
NC_000012.12:g.112477719A>G
CM000674.2:g.112477719A>G
NC_000012.11:g.112915523A>G
CM000674.1:g.112915523A>G
NC_000012.10:g.111399906A>G
NG_007459.1:g.63988A>G
NM_002834.3:c.922A>G
NM_080601.1:c.922A>G
NM_001330437.1:c.922A>G
NM_080601.2:c.922A>G
ENST00000351677.6:c.922A>G
ENST00000392597.5:c.922A>G
ENST00000635625.1:n.922A>G

Pathogenic

Met criteria codes 6
PS2_Very Strong PP1_Strong PS3 PP3 PP2 PM2
Not Met criteria codes 1
PM6

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.922A>G (p.Asn308Asp) variant in PTPN11 has been reported in the literature as a confirmed and unconfirmed de novo occurrence in 2 patients with clinical features of a RASopathy (PS2_VeryStrong; PMID 20979190, and 11704759, 22465605). The variant has co-segregated with disease in more than 7 family members (PP1_Strong; PMID: 11992261). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The 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). Computational prediction tools and conservation analysis suggest that the p.Asn308Asp variant may impact the protein (PP3). Additionally, at least 2 functional studies have been concordant in showing that this variant may be deleterious to the protein (PS3; PMID 14974085, 15987685, 19509418, 20308328). 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): PP2, PP3, PM2, PP1_Strong, PS2_VeryStrong, PS3.
Met criteria codes
PS2_Very Strong
The p.Asn308Asp variant in PTPN11 has been reported in the literature as a confirmed and unconfirmed de novo occurrence in 2 patients with clinical features of a RASopathy (PS2, PM6; PMID 20979190, and 11704759, 22465605).
PP1_Strong
The variant has co-segregated with disease in more than 7 family members (PP1_Strong; PMID: 11992261).
PS3
Additionally, at least 2 functional studies have been concordant in showing that this variant may be deleterious to the protein (PS3; PMID 14974085, 15987685, 19509418, 20308328).
PP3
Computational prediction tools and conservation analysis suggest that the p.Asn308Asp variant may impact the protein (PP3).
PP2
The 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)
PM2
This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org).
Not Met criteria codes
PM6
The p.Asn308Asp variant in PTPN11 has been reported in the literature as a confirmed and unconfirmed de novo occurrence in 2 patients with clinical features of a RASopathy (PS2, PM6; PMID 20979190, and 11704759, 22465605).
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