NM_005633.4(SOS1):c.1627T>C (p.Ser543Pro) AND not provided

Germline classification:: Uncertain significance (2 submissions)
Last evaluated:: Dec 1, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000588660.9

Allele description [Variation Report for NM_005633.4(SOS1):c.1627T>C (p.Ser543Pro)]

NM_005633.4(SOS1):c.1627T>C (p.Ser543Pro)

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.1627T>C (p.Ser543Pro)

HGVS:

NC_000002.12:g.39022801A>G
NG_007530.1:g.102663T>C
NM_001382394.1:c.1606T>C
NM_001382395.1:c.1627T>C
NM_005633.4:c.1627T>CMANE SELECT
NP_001369323.1:p.Ser536Pro
NP_001369324.1:p.Ser543Pro
NP_005624.2:p.Ser543Pro
NP_005624.2:p.Ser543Pro
LRG_754t1:c.1627T>C
LRG_754:g.102663T>C
LRG_754p1:p.Ser543Pro
NC_000002.11:g.39249942A>G
NM_005633.3:c.1627T>C

Protein change:

S536P

Links:

dbSNP: rs981234810

NCBI 1000 Genomes Browser:

rs981234810

Molecular consequence:

NM_001382394.1:c.1606T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001382395.1:c.1627T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005633.4:c.1627T>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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zinc finger protein 226 isoform a [Homo sapiens]
zinc finger protein 226 isoform a [Homo sapiens]
gi|977357030|ref|NP_057528.2|

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000698613	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Jun 19, 2017)	germline	clinical testing	LabCorp Variant Classification Summary - May 2015.docx, Citation Link,
SCV004702363	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Dec 1, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000698613

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Jun 19, 2017)

germline

clinical testing

LabCorp Variant Classification Summary - May 2015.docx,

Citation Link,

SCV004702363

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Uncertain significance
(Dec 1, 2023)

germline

clinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000698613.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Variant summary: The SOS1 c.1627T>C (p.Ser543Pro) variant located in the PH domain-like domain (via InterPro) involves the alteration of a conserved nucleotide and 3/4 in silico tools predict a damaging outcome. This variant was found in 3/214708 control chromosomes (gnomAD) at a frequency of 0.000014, which does not exceed the estimated maximal expected allele frequency of a pathogenic SOS1 variant (0.00003). A clinical diagnostic laboratory classified this variant as uncertain significance. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. Because of the absence of clinical information and the lack of functional studies, the variant is classified as a "Variant of Uncertain Significance (VUS)," until additional information becomes available.

#	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

From CeGaT Center for Human Genetics Tuebingen, SCV004702363.8

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	not provided

Description

SOS1: PM1, PM2, PP3

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

Last Updated: Nov 3, 2024

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