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NM_005633.4(SOS1):c.1645A>G (p.Thr549Ala) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jun 25, 2018
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000681394.1

Allele description [Variation Report for NM_005633.4(SOS1):c.1645A>G (p.Thr549Ala)]

NM_005633.4(SOS1):c.1645A>G (p.Thr549Ala)

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_005633.4(SOS1):c.1645A>G (p.Thr549Ala)
HGVS:
  • NC_000002.12:g.39022783T>C
  • NG_007530.1:g.102681A>G
  • NM_001382394.1:c.1624A>G
  • NM_001382395.1:c.1645A>G
  • NM_005633.4:c.1645A>GMANE SELECT
  • NP_001369323.1:p.Thr542Ala
  • NP_001369324.1:p.Thr549Ala
  • NP_005624.2:p.Thr549Ala
  • NP_005624.2:p.Thr549Ala
  • LRG_754t1:c.1645A>G
  • LRG_754:g.102681A>G
  • LRG_754p1:p.Thr549Ala
  • NC_000002.11:g.39249924T>C
  • NM_005633.3(SOS1):c.1645A>G
  • NM_005633.3:c.1645A>G
  • p.Thr549Ala
Protein change:
T542A
Links:
dbSNP: rs1558474335
NCBI 1000 Genomes Browser:
rs1558474335
Molecular consequence:
  • NM_001382394.1:c.1624A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382395.1:c.1645A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005633.4:c.1645A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000808857GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Uncertain significance
(Jun 25, 2018)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000808857.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

A variant of uncertain significance has been identified in the SOS1 gene. The T549A variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The T549A variant is not observed in large population cohorts (Lek et al., 2016). The T549A variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. In addition, missense variants in the same and in nearby residues have been reported in the Human Gene Mutation Database in individuals with Noonan syndrome (Stenson et al., 2014). However, in-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: Jun 9, 2022