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_007373.3(SHOC2):c.4A>G (p.Ser2Gly)

CA118524

6821 (ClinVar)

Gene: SHOC2
Condition: Noonan syndrome-like disorder with loose anagen hair 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 39b0e509-abdb-415d-87bd-98b7310bb1c0
Approved on: 2017-04-03
Published on: 2018-12-10

HGVS expressions

NM_007373.3:c.4A>G
NM_007373.3(SHOC2):c.4A>G (p.Ser2Gly)
NC_000010.11:g.110964362A>G
CM000672.2:g.110964362A>G
NC_000010.10:g.112724120A>G
CM000672.1:g.112724120A>G
NC_000010.9:g.112714110A>G
NG_028922.1:g.49820A>G
NM_001269039.1:c.4A>G
NM_001269039.2:c.4A>G
NM_001324336.1:c.4A>G
NM_001324337.1:c.4A>G
NR_136749.1:n.116-21266A>G
ENST00000265277.9:c.4A>G
ENST00000369452.8:c.4A>G
ENST00000480155.1:n.488A>G
ENST00000489390.1:n.56-36053A>G
ENST00000489783.1:n.382A>G
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Pathogenic

Met criteria codes 5
PS3 PS4 PP2 PM2 PS2_Very Strong

Evidence Links 6

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.4A>G (p.Ser2Gly) variant in SHOC2 has been reported as a confirmed de novo occurrence in multiple patients with clinical features of a RASopathy (PS2_VeryStrong; Partners LMM, Institute of Human Genetics, Otto von Guericke University Magdeburg, APHP-Robert Debré Hospital internal data; GTR ID's: 21766, 506381, 28338; ClinVar SCV000062456.5, SCV000209051.10, SCV000263045.1 PMID 19684605, 21548061, 23918763, 22528146). The p.Ser2Gly variant has been identified in at least 5 independent occurrences in patients with clinical features of a RASopathy (PS4; Institute of Human Genetics, Otto von Guericke University Magdeburg, APHP-Robert Debré Hospital internal data GTR ID's: 506381, 28338; PMID: 25563136, 24458587). In vitro functional studies provide some evidence that the p.Ser2Gly variant may impact protein function (PS3; PMID: 19684605). This variant was absent from large population studies (PM2; ExAC, http://exac.broadinstitute.org). The variant is located in the SHOC2 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, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2_VeryStrong, PS3, PS4, PM2, PP2.
Met criteria codes
PS3
In vitro functional studies provide some evidence that the p.Ser2Gly variant may impact protein function (PS3; PMID: 19684605).

PS4
The p.Ser2Gly variant has been identified in at least 5 independent occurrences in patients with clinical features of a RASopathy (PS4; Institute of Human Genetics, Otto von Guericke University Magdeburg, APHP-Robert Debré Hospital internal data GTR ID's: 506381, 28338; PMID: 25563136, 24458587)

PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2_Very Strong
The c.4A>G (p.Ser2Gly) variant in SHOC2 has been reported as a confirmed de novo occurrence in a patient with clinical features of a RASopathy (PS2_VeryStrong; Partners LMM, Institute of Human Genetics, Otto von Guericke University Magdeburg, APHP-Robert Debré Hospital internal data; GTR ID's: 21766, 506381, 28338; ClinVar SCV000062456.5, SCV000209051.10, SCV000263045.1 PMID 19684605, 21548061, 23918763, 22528146).

Curation History
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