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NM_002880.4(RAF1):c.917C>T (p.Ser306Leu) AND Noonan syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Dec 5, 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:
RCV001249756.4

Allele description [Variation Report for NM_002880.4(RAF1):c.917C>T (p.Ser306Leu)]

NM_002880.4(RAF1):c.917C>T (p.Ser306Leu)

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.917C>T (p.Ser306Leu)
HGVS:
  • NC_000003.12:g.12600225G>A
  • NG_007467.1:g.68955C>T
  • NM_001354689.3:c.977C>T
  • NM_001354690.3:c.917C>T
  • NM_001354691.3:c.674C>T
  • NM_001354692.3:c.674C>T
  • NM_001354693.3:c.818C>T
  • NM_001354694.3:c.734C>T
  • NM_001354695.3:c.575C>T
  • NM_002880.4:c.917C>TMANE SELECT
  • NP_001341618.1:p.Ser326Leu
  • NP_001341619.1:p.Ser306Leu
  • NP_001341620.1:p.Ser225Leu
  • NP_001341621.1:p.Ser225Leu
  • NP_001341622.1:p.Ser273Leu
  • NP_001341623.1:p.Ser245Leu
  • NP_001341624.1:p.Ser192Leu
  • NP_002871.1:p.Ser306Leu
  • NP_002871.1:p.Ser306Leu
  • LRG_413t1:c.917C>T
  • LRG_413t2:c.977C>T
  • LRG_413:g.68955C>T
  • LRG_413p1:p.Ser306Leu
  • LRG_413p2:p.Ser326Leu
  • NC_000003.11:g.12641724G>A
  • NM_002880.3:c.917C>T
  • NR_148940.3:n.1248C>T
  • NR_148941.3:n.1248C>T
  • NR_148942.3:n.1248C>T
Protein change:
S192L
Links:
dbSNP: rs886041231
NCBI 1000 Genomes Browser:
rs886041231
Molecular consequence:
  • NM_001354689.3:c.977C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354690.3:c.917C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354691.3:c.674C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354692.3:c.674C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354693.3:c.818C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354694.3:c.734C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354695.3:c.575C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002880.4:c.917C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148940.3:n.1248C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148941.3:n.1248C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148942.3:n.1248C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:
Noonan syndrome (NS)
Synonyms:
Noonan's syndrome; Pseudo-Turner syndrome
Identifiers:
MONDO: MONDO:0018997; MeSH: D009634; MedGen: C0028326; OMIM: PS163950

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001423789Illumina Laboratory Services, Illumina
criteria provided, single submitter

(ICSLVariantClassificationCriteria RUGD 01 April 2020)		Uncertain significance
(Dec 5, 2019) 		unknownclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From Illumina Laboratory Services, Illumina, SCV001423789.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The RAF1 c.917C>T (p.Ser306Leu) variant is a missense variant. A literature search was performed for the gene, cDNA change, and amino acid change. No publications were found based on this search. This variant is reported at a frequency of 0.000116 in the Latino population of the Genome Aggregation Database. Noonan syndrome is associated with variable expressivity and mild expression can be overlooked. Based on the limited evidence, the p.Ser306Leu variant is classified as a variant of unknown significance for Noonan syndrome.

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

Last Updated: Sep 29, 2024