NM_002880.4(RAF1):c.770C>T (p.Ser257Leu) AND Noonan syndrome 1

Germline classification:: Pathogenic (3 submissions)
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:: RCV000856803.11

Allele description [Variation Report for NM_002880.4(RAF1):c.770C>T (p.Ser257Leu)]

NM_002880.4(RAF1):c.770C>T (p.Ser257Leu)

Gene:

RAF1:Raf-1 proto-oncogene, serine/threonine kinase [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3p25.2

Genomic location:

Preferred name:

NM_002880.4(RAF1):c.770C>T (p.Ser257Leu)

Other names:

p.S257L:TCG>TTG; NM_002880.3(RAF1):c.770C>T

HGVS:

NC_000003.12:g.12604200G>A
NG_007467.1:g.64980C>T
NM_001354689.3:c.770C>T
NM_001354690.3:c.770C>T
NM_001354691.3:c.527C>T
NM_001354692.3:c.527C>T
NM_001354693.3:c.671C>T
NM_001354694.3:c.527C>T
NM_001354695.3:c.428C>T
NM_002880.4:c.770C>TMANE SELECT
NP_001341618.1:p.Ser257Leu
NP_001341619.1:p.Ser257Leu
NP_001341620.1:p.Ser176Leu
NP_001341621.1:p.Ser176Leu
NP_001341622.1:p.Ser224Leu
NP_001341623.1:p.Ser176Leu
NP_001341624.1:p.Ser143Leu
NP_002871.1:p.Ser257Leu
NP_002871.1:p.Ser257Leu
LRG_413t1:c.770C>T
LRG_413t2:c.770C>T
LRG_413:g.64980C>T
LRG_413p1:p.Ser257Leu
LRG_413p2:p.Ser257Leu
NC_000003.11:g.12645699G>A
NM_001354689.1:c.770C>T
NM_002880.2:c.770C>T
NM_002880.3:c.770C>T
NM_002880.4:c.770C>T
NR_148940.3:n.1101C>T
NR_148941.3:n.1101C>T
NR_148942.3:n.1101C>T
P04049:p.Ser257Leu

Protein change:

S143L; SER257LEU

Links:

UniProtKB: P04049#VAR_037808; OMIM: 164760.0001; dbSNP: rs80338796

NCBI 1000 Genomes Browser:

rs80338796

Molecular consequence:

NM_001354689.3:c.770C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354690.3:c.770C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354691.3:c.527C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354692.3:c.527C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354693.3:c.671C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354694.3:c.527C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354695.3:c.428C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002880.4:c.770C>T - missense variant - [Sequence Ontology: SO:0001583]
NR_148940.3:n.1101C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148941.3:n.1101C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148942.3:n.1101C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Noonan syndrome 1 (NS1)
Synonyms:: Turner Syndrome, Male; Turner phenotype with normal karyotype; Female pseudo-Turner syndrome
Identifiers:: MONDO: MONDO:0008104; MedGen: C4551602; Orphanet: 648; OMIM: 163950

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000999369	Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV003840161	Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand	no assertion criteria provided	Pathogenic	unknown	research
SCV004190086	Molecular Genetics, Centre for Human Genetics	no assertion criteria provided	Pathogenic	de novo	clinical testing

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000999369

Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

unknown

clinical testing

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

SCV003840161

Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand

no assertion criteria provided

Pathogenic

unknown

research

SCV004190086

Molecular Genetics, Centre for Human Genetics

no assertion criteria provided

Pathogenic

de novo

clinical testing

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	de novo	yes	3	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	yes	2	not provided	not provided	2	not provided	clinical testing, research

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 Institute for Genomic Statistics and Bioinformatics, University Hospital Bonn, SCV000999369.1

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

From Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand, SCV003840161.1

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

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

From Molecular Genetics, Centre for Human Genetics, SCV004190086.1

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

#	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		3	not provided	not provided	not provided

Last Updated: Apr 20, 2024

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