NM_005633.4(SOS1):c.1642A>C (p.Ser548Arg) AND Noonan syndrome 4

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Feb 26, 2024
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:: RCV002054544.10

Allele description [Variation Report for NM_005633.4(SOS1):c.1642A>C (p.Ser548Arg)]

NM_005633.4(SOS1):c.1642A>C (p.Ser548Arg)

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.1642A>C (p.Ser548Arg)

Other names:

p.S548R:AGT>CGT; NM_005633.3(SOS1):c.1642A>C

HGVS:

NC_000002.12:g.39022786T>G
NG_007530.1:g.102678A>C
NM_001382394.1:c.1621A>C
NM_001382395.1:c.1642A>C
NM_005633.4:c.1642A>CMANE SELECT
NP_001369323.1:p.Ser541Arg
NP_001369324.1:p.Ser548Arg
NP_005624.2:p.Ser548Arg
NP_005624.2:p.Ser548Arg
NP_005624.2:p.Ser548Arg
LRG_754t1:c.1642A>C
LRG_754:g.102678A>C
LRG_754p1:p.Ser548Arg
NC_000002.11:g.39249927T>G
NM_005633.3:c.1642A>C
Q07889:p.Ser548Arg
c.1642A>C

Protein change:

S541R

Links:

UniProtKB: Q07889#VAR_030432; dbSNP: rs397517149

NCBI 1000 Genomes Browser:

rs397517149

Molecular consequence:

NM_001382394.1:c.1621A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001382395.1:c.1642A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_005633.4:c.1642A>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Noonan syndrome 4 (NS4)
Synonyms:: NOONAN SYNDROME WITH PIGMENTED VILLONODULAR SYNOVITIS; NL/MGCLS
Identifiers:: MONDO: MONDO:0012547; MedGen: C1853120; Orphanet: 648; OMIM: 610733

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Profile neighbors for GEO Profiles (Select 105192744) (39)
GEO Profiles
Profile neighbors for GEO Profiles (Select 105192996) (42)
GEO Profiles
BLACAT1 BLACAT1 overlapping LEMD1 locus [Homo sapiens]
BLACAT1 BLACAT1 overlapping LEMD1 locus [Homo sapiens]
Gene ID:101669762

Gene
Gene Links for GEO Profiles (Select 105218060) (1)
Gene
B4GALT6 beta-1,4-galactosyltransferase 6 [Homo sapiens]
B4GALT6 beta-1,4-galactosyltransferase 6 [Homo sapiens]
Gene ID:9331

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002320777	Provincial Medical Genetics Program of British Columbia, University of British Columbia	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jan 1, 2022)	de novo	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV005049882	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Feb 26, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002320777

Provincial Medical Genetics Program of British Columbia, University of British Columbia

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jan 1, 2022)

de novo

clinical testing

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

SCV005049882

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Feb 26, 2024)

unknown

clinical testing

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

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Provincial Medical Genetics Program of British Columbia, University of British Columbia, SCV002320777.1

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

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

From Baylor Genetics, SCV005049882.1

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

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

Last Updated: Nov 3, 2024

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