NM_005633.4(SOS1):c.1705C>G (p.Leu569Val) AND not specified

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Jul 5, 2016
Review status:: criteria provided, conflicting classifications

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:: RCV000223591.7

Allele description [Variation Report for NM_005633.4(SOS1):c.1705C>G (p.Leu569Val)]

NM_005633.4(SOS1):c.1705C>G (p.Leu569Val)

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.1705C>G (p.Leu569Val)

Other names:

NM_005633.3(SOS1):c.1705C>G

HGVS:

NC_000002.12:g.39022723G>C
NG_007530.1:g.102741C>G
NM_001382394.1:c.1684C>G
NM_001382395.1:c.1705C>G
NM_005633.4:c.1705C>GMANE SELECT
NP_001369323.1:p.Leu562Val
NP_001369324.1:p.Leu569Val
NP_005624.2:p.Leu569Val
NP_005624.2:p.Leu569Val
LRG_754t1:c.1705C>G
LRG_754:g.102741C>G
LRG_754p1:p.Leu569Val
NC_000002.11:g.39249864G>C
NM_005633.3:c.1705C>G
Q07889:p.Leu569Val
p.LEU569VAL

Protein change:

L562V

Links:

UniProtKB: Q07889#VAR_066051; dbSNP: rs200786705

NCBI 1000 Genomes Browser:

rs200786705

Molecular consequence:

NM_001382394.1:c.1684C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001382395.1:c.1705C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_005633.4:c.1705C>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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hypothetical protein Naga_100081g21 [Nannochloropsis gaditana]
hypothetical protein Naga_100081g21 [Nannochloropsis gaditana]
gi|585101001|gb|EWM21003.1||gnl|WGS |Naga_100081g21.750

Protein
Oregano - LiverTox
Oregano - LiverTox
PGM3 [Aquila chrysaetos chrysaetos]
PGM3 [Aquila chrysaetos chrysaetos]
Gene ID:115349684

Gene
CHS2 [Candida albicans SC5314]
CHS2 [Candida albicans SC5314]
Gene ID:3641893

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000270858	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Likely benign (Dec 16, 2015)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 21387466, 24033266
SCV000615372	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Uncertain significance (Jul 5, 2016)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 19953625, 21387466, 26467025

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000270858

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Likely benign
(Dec 16, 2015)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

SCV000615372

Athena Diagnostics

criteria provided, single submitter

(Athena Diagnostics Criteria)

Uncertain significance
(Jul 5, 2016)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	1	1	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Tumor spectrum in children with Noonan syndrome and SOS1 or RAF1 mutations.

Denayer E, Devriendt K, de Ravel T, Van Buggenhout G, Smeets E, Francois I, Sznajer Y, Craen M, Leventopoulos G, Mutesa L, Vandecasseye W, Massa G, Kayserili H, Sciot R, Fryns JP, Legius E.

Genes Chromosomes Cancer. 2010 Mar;49(3):242-52. doi: 10.1002/gcc.20735.

PubMed [citation]

PMID:: 19953625

See all PubMed Citations (4)

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000270858.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (2)

Description

p.Leu569Val in exon 10 of SOS1: This variant is not expected to have clinical s ignificance because it has been identified in 31/66714 European chromosomes and 6/16504 South Asian chromosomes by the Exome Aggregation Consortium (ExAC, http: //exac.broadinstitute.org/; dbSNP rs200786705). It has also been reported in 1 u naffected adult in the homozygous state (Lepri 2011).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		1	not provided	1	not provided

From Athena Diagnostics, SCV000615372.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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