NM_001354689.3(RAF1):c.768G>T (p.Arg256Ser) AND not provided

Clinical significance:Pathogenic (Last evaluated: Mar 19, 2019)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000159072.4

Allele description [Variation Report for NM_001354689.3(RAF1):c.768G>T (p.Arg256Ser)]

NM_001354689.3(RAF1):c.768G>T (p.Arg256Ser)

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_001354689.3(RAF1):c.768G>T (p.Arg256Ser)
Other names:
p.R256S:AGG>AGT; NM_002880.3(RAF1):c.768G>T
HGVS:
  • NC_000003.12:g.12604202C>A
  • NG_007467.1:g.64978G>T
  • NM_001354689.3:c.768G>TMANE SELECT
  • NM_001354690.2:c.768G>T
  • NM_001354691.2:c.525G>T
  • NM_001354692.2:c.525G>T
  • NM_001354693.2:c.669G>T
  • NM_001354694.2:c.525G>T
  • NM_001354695.2:c.426G>T
  • NM_002880.3:c.768G>T
  • NP_001341618.1:p.Arg256Ser
  • NP_001341619.1:p.Arg256Ser
  • NP_001341620.1:p.Arg175Ser
  • NP_001341621.1:p.Arg175Ser
  • NP_001341622.1:p.Arg223Ser
  • NP_001341623.1:p.Arg175Ser
  • NP_001341624.1:p.Arg142Ser
  • NP_002871.1:p.Arg256Ser
  • LRG_413t1:c.768G>T
  • LRG_413t2:c.768G>T
  • LRG_413:g.64978G>T
  • LRG_413p1:p.Arg256Ser
  • LRG_413p2:p.Arg256Ser
  • NC_000003.11:g.12645701C>A
  • NR_148940.2:n.1099G>T
  • NR_148941.2:n.1099G>T
  • NR_148942.2:n.1099G>T
  • P04049:p.Arg256Ser
  • c.768G>T
Protein change:
R142S
Links:
UniProtKB: P04049#VAR_037807; dbSNP: rs397516826
NCBI 1000 Genomes Browser:
rs397516826
Molecular consequence:
  • NM_001354689.3:c.768G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354690.2:c.768G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354691.2:c.525G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354692.2:c.525G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354693.2:c.669G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354694.2:c.525G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354695.2:c.426G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002880.3:c.768G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148940.2:n.1099G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148941.2:n.1099G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148942.2:n.1099G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000209014GeneDxcriteria provided, single submitter
Pathogenic
(Mar 19, 2019)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000209014.11

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

Description

Published functional studies demonstrate a damaging effect on protein localization and activity (Molzan et al., 2010); Identified in patients with Noonan syndrome and/or hypertrophic cardiomyopathy referred for genetic testing at GeneDx and in published literature (Pandit et al., 2007); Reported in ClinVar as pathogenic by another clinical laboratory and the ClinGen RASopathy Variant Curation Expert Panel (ClinVar Variant ID# 40599; SCV000616377.3, SCV000061363.5; Landrum et al., 2016); Not observed in large population cohorts (Lek et al., 2016); Located in the CR2 critical functional domain; The majority of missense variants in this gene are considered pathogenic (Stenson et al., 2014); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect

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

Last Updated: Sep 29, 2021

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