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_005633.3(SOS1):c.2536G>A (p.Glu846Lys)

CA261734

40706 (ClinVar)

Gene: SOS1
Condition: Noonan syndrome
Inheritance Mode: Autosomal dominant inheritance
UUID: f2a2e5e9-f8ba-43a4-9776-40b192ce87cf
Approved on: 2017-04-03
Published on: 2018-12-10

HGVS expressions

NM_005633.3:c.2536G>A
NM_005633.3(SOS1):c.2536G>A (p.Glu846Lys)
ENST00000395038.6:c.2536G>A
ENST00000402219.6:c.2536G>A
ENST00000426016.5:c.2536G>A
ENST00000474390.1:n.332G>A
NC_000002.12:g.39007168C>T
CM000664.2:g.39007168C>T
NC_000002.11:g.39234309C>T
CM000664.1:g.39234309C>T
NC_000002.10:g.39087813C>T
NG_007530.1:g.118296G>A
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Pathogenic

Met criteria codes 6
PM6 PM2 PM1 PS3 PP3 PP2
Not Met criteria codes 1
PS4

Evidence Links 3

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.2536G>A (p.Glu846Lys) variant in SOS1 has been reported in the literature as an unconfirmed de novo occurrence in a patient with clinical features of a RASopathy (PM6; PMID 23673306). It has also been reported in a patient diagnosed with HCM (PMID 22555271). In vitro functional studies provide some evidence that the p.Glu846Lys variant may impact protein function (PS3; PMID 17143285). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). Computational prediction tools and conservation analysis suggest that the p.Glu846Lys variant may impact the protein (PP3). The variant is located in the SOS1 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). Furthermore, the variant is in a location that has been defined to be a mutational hotspot or domain of SOS1 (PM1; PMID 21387466). 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, PM1, PM2, PM6, PS3.
Met criteria codes
PM6
The c.2536G>A (p.Glu846Lys) variant in SOS1 has been reported in the literature as an unconfirmed de novo occurrence in a patient with clinical features of a RASopathy (PM6; PMID 23673306).

PM2
This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org).
PM1
Furthermore, the variant is in a location that has been defined to be a mutational hotspot or domain of SOS1 (PM1; PMID 21387466).
PS3
In vitro functional studies provide some evidence that the p.Glu846Lys variant may impact protein function (PS3; PMID 17143285)

PP3
Computational prediction tools and conservation analysis suggest that the p.Glu846Lys variant may impact the protein (PP3).
PP2
The variant is located in the SOS1 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).
Not Met criteria codes
PS4
Curation History
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