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.3600C>G (p.Asp1200Glu)

CA297240

40733 (ClinVar)

Gene: SOS1
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: 9b08e55f-32bb-4cc3-bfff-815c445525b7
Approved on: 2019-06-27
Published on: 2019-06-28

HGVS expressions

NM_005633.3:c.3600C>G
NM_005633.3(SOS1):c.3600C>G (p.Asp1200Glu)
NC_000002.12:g.38986226G>C
CM000664.2:g.38986226G>C
NC_000002.11:g.39213367G>C
CM000664.1:g.39213367G>C
NC_000002.10:g.39066871G>C
NG_007530.1:g.139238C>G
ENST00000395038.6:c.3555C>G
ENST00000402219.6:c.3600C>G
ENST00000426016.5:c.3600C>G
ENST00000469581.1:n.343C>G
More

Likely Benign

Met criteria codes 3
BS1 BP5 BP4
Not Met criteria codes 20
BS2 BS4 BS3 BP7 BP1 BP2 BP3 PS4 PS3 PS2 PS1 PP2 PP3 PP1 BA1 PM2 PM6 PM1 PM4 PM5

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.3600C>G (p.Asp1200Glu) variant in the SOS1 gene has been identified in at least 6 individuals without detailed phenotypic information as well as one patient with an alternative molecular basis for disease in the BRAF gene (BP5; EGL, Invitae, GeneDx internal data, GTR Lab ID: 500060, 500031, 26957; SCV000854873.1, SCV000553268.3, SCV000209087.11). The filtering allele frequency of the c.3600C>G (p.Asp1200Glu) variant is 0.025% for European (non-Finnish) exomes by the gnomAD database (40/251300 with 95% CI) which is strong evidence to suggest that the variant may be benign based on thresholds defined by the ClinGen RASopathy Expert Panel for autosomal dominant RASopathy variants (BS1). Of note, the c.3600C>A change that also results in p.Asp1200Glu has been identified in one patient with a RASopathy but this variant has not met criteria to be classified as pathogenic and therefore PM5 is not met (Partners LMM internal data; GTR Lab ID: 21766; SCV000062231.5). Computational prediction tools and conservation analysis suggest that the p.Asp1200Glu variant does not impact the protein (BP4). In summary, this variant meets criteria to be classified as likely benign. RASopathy-specific ACMG/AMP criteria applied (PMID:29493581): BS1, BP4, BP5.
Met criteria codes
BS1
This variant has been observed in 42/126584 (0.00033)
BP5
GeneDx: seen in patient with p.Gly596Val in BRAF
BP4
REVEL score of 0.207 which is low and only mutation taster is predicting Path. There are several mammals including the chinchilla and the horse.
Not Met criteria codes
BS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP7
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
EGL: Found varint in het state from 2 short stature panels but neither case had detailed clinical information to molecularly diagnose the patient with a RASopathy. Invitae: We saw 3600C>G in 3 juvenile patients without a provided phenotype and one adult without a provided phenotype,

PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
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
PP3
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
BA1
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
PM6
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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