NM_005633.3(SOS1):c.2010G>C (p.Leu670Phe) AND Rasopathy

Clinical significance:Benign (Last evaluated: Apr 18, 2017)

Review status:3 stars out of maximum of 4 stars

reviewed by expert panel

Based on:
2 submissions [Details]
Record status:
current
Accession:
RCV000518853.5

Allele description [Variation Report for NM_005633.3(SOS1):c.2010G>C (p.Leu670Phe)]

NM_005633.3(SOS1):c.2010G>C (p.Leu670Phe)

Gene:
SOS1:SOS Ras/Rac guanine nucleotide exchange factor 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
2p22.1
Genomic location:
Preferred name:
NM_005633.3(SOS1):c.2010G>C (p.Leu670Phe)
Other names:
NM_005633.3(SOS1):c.2010G>C
HGVS:
  • NC_000002.12:g.39013920C>G
  • NG_007530.1:g.111544G>C
  • NM_005633.3:c.2010G>C
  • NP_005624.2:p.Leu670Phe
  • LRG_754t1:c.2010G>C
  • LRG_754:g.111544G>C
  • LRG_754p1:p.Leu670Phe
  • NC_000002.11:g.39241061C>G
Protein change:
L670F
Links:
dbSNP: rs200712930
NCBI 1000 Genomes Browser:
rs200712930
Molecular consequence:
  • NM_005633.3:c.2010G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Rasopathy
Synonyms:
rasopathies; Noonan spectrum disorder
Identifiers:
MONDO: MONDO:0021060; MedGen: CN166718

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000616515ClinGen RASopathy Variant Curation Expert Panelreviewed by expert panel
Benign
(Apr 18, 2017)
germlinecuration

Citation Link,

SCV000776847Invitaecriteria provided, single submitter
Likely benign
(Mar 16, 2020)
germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing, curation

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240-242.

PubMed [citation]
PMID:
28492532
PMCID:
PMC5632818

Details of each submission

From ClinGen RASopathy Variant Curation Expert Panel, SCV000616515.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The filtering allele frequency of the c.2010G>C (p.Leu670Phe) variant in the SOS1 gene is 0.055% (9/8572) of East Asian chromosomes by the Exome Aggregation Consortium, which is a high enough frequency to be classified as benign based on thresholds defined by the ClinGen RASopathy Expert Panel (BA1; PMID:29493581)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

From Invitae, SCV000776847.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Aug 27, 2021

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