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NM_005633.4(SOS1):c.1829T>C (p.Ile610Thr) AND not specified

Germline classification:
Likely benign (1 submission)
Last evaluated:
Mar 18, 2019
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:
RCV001192789.1

Allele description [Variation Report for NM_005633.4(SOS1):c.1829T>C (p.Ile610Thr)]

NM_005633.4(SOS1):c.1829T>C (p.Ile610Thr)

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.1829T>C (p.Ile610Thr)
HGVS:
  • NC_000002.12:g.39022599A>G
  • NG_007530.1:g.102865T>C
  • NM_001382394.1:c.1808T>C
  • NM_001382395.1:c.1829T>C
  • NM_005633.4:c.1829T>CMANE SELECT
  • NP_001369323.1:p.Ile603Thr
  • NP_001369324.1:p.Ile610Thr
  • NP_005624.2:p.Ile610Thr
  • NP_005624.2:p.Ile610Thr
  • LRG_754t1:c.1829T>C
  • LRG_754:g.102865T>C
  • LRG_754p1:p.Ile610Thr
  • NC_000002.11:g.39249740A>G
  • NM_005633.3:c.1829T>C
Protein change:
I603T
Links:
dbSNP: rs776146535
NCBI 1000 Genomes Browser:
rs776146535
Molecular consequence:
  • NM_001382394.1:c.1808T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001382395.1:c.1829T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_005633.4:c.1829T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001361134Women's Health and Genetics/Laboratory Corporation of America, LabCorp
criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)		Likely benign
(Mar 18, 2019) 		germlineclinical testing

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

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

Mutational analysis of SOS1 gene in acute myeloid leukemia.

Tanizaki R, Katsumi A, Kiyoi H, Kunishima S, Iwasaki T, Ishikawa Y, Kobayashi M, Abe A, Matsushita T, Watanabe T, Kojima T, Kaibuchi K, Kojima S, Naoe T.

Int J Hematol. 2008 Nov;88(4):460-462. doi: 10.1007/s12185-008-0185-1. Epub 2008 Oct 30. No abstract available.

PubMed [citation]
PMID:
18972187

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV001361134.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

Variant summary: SOS1 c.1829T>C (p.Ile610Thr) results in a non-conservative amino acid change located in the Ras-like guanine nucleotide exchange factor, N-terminal of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 8.3e-05 in 276230 control chromosomes. The observed variant frequency is approximately 2.8 fold of the estimated maximal expected allele frequency for a pathogenic variant in SOS1 causing Noonan Syndrome and Related Conditions phenotype (3e-05), strongly suggesting that the variant is benign. c.1829T>C has not been reported in the literature in individuals affected with Noonan Syndrome and Related Conditions. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as likely benign.

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

Last Updated: Oct 20, 2024