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NM_002880.4(RAF1):c.856G>A (p.Glu286Lys) AND not specified

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
May 1, 2015
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:
RCV000412986.1

Allele description [Variation Report for NM_002880.4(RAF1):c.856G>A (p.Glu286Lys)]

NM_002880.4(RAF1):c.856G>A (p.Glu286Lys)

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.856G>A (p.Glu286Lys)
HGVS:
  • NC_000003.12:g.12600394C>T
  • NG_007467.1:g.68786G>A
  • NM_001354689.3:c.916G>A
  • NM_001354690.3:c.856G>A
  • NM_001354691.3:c.613G>A
  • NM_001354692.3:c.613G>A
  • NM_001354693.3:c.757G>A
  • NM_001354694.3:c.673G>A
  • NM_001354695.3:c.514G>A
  • NM_002880.4:c.856G>AMANE SELECT
  • NP_001341618.1:p.Glu306Lys
  • NP_001341619.1:p.Glu286Lys
  • NP_001341620.1:p.Glu205Lys
  • NP_001341621.1:p.Glu205Lys
  • NP_001341622.1:p.Glu253Lys
  • NP_001341623.1:p.Glu225Lys
  • NP_001341624.1:p.Glu172Lys
  • NP_002871.1:p.Glu286Lys
  • NP_002871.1:p.Glu286Lys
  • LRG_413t1:c.856G>A
  • LRG_413t2:c.916G>A
  • LRG_413:g.68786G>A
  • LRG_413p1:p.Glu286Lys
  • LRG_413p2:p.Glu306Lys
  • NC_000003.11:g.12641893C>T
  • NM_002880.3:c.856G>A
  • NR_148940.3:n.1187G>A
  • NR_148941.3:n.1187G>A
  • NR_148942.3:n.1187G>A
Protein change:
E172K
Links:
dbSNP: rs147453956
NCBI 1000 Genomes Browser:
rs147453956
Molecular consequence:
  • NM_001354689.3:c.916G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354690.3:c.856G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354691.3:c.613G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354692.3:c.613G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354693.3:c.757G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354694.3:c.673G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354695.3:c.514G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002880.4:c.856G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148940.3:n.1187G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148941.3:n.1187G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148942.3:n.1187G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000490979GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Uncertain significance
(May 1, 2015)
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, SCV000490979.1

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

Description

The E286K variant has not been published as a pathogenic variant nor has it been reported as a benign polymorphism to our knowledge. The E286K variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. The E286K variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations, however, the 1000 Genomes Project reports E286K was observed in 2/1008 (0.2%) alleles from individuals of East Asian ancestry, indicating it may be a rare (benign) variant in this population. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Finally, no missense variants in nearby residues have been reported in the Human Gene Mutation Database in association with cardiomyopathy (Stenson et al., 2014), suggesting this region of the protein may be tolerant of change. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant

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

Last Updated: Sep 29, 2024