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NM_002880.4(RAF1):c.1687C>T (p.Arg563Ter) AND RAF1-related disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 17, 2023
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:
RCV004536103.1

Allele description [Variation Report for NM_002880.4(RAF1):c.1687C>T (p.Arg563Ter)]

NM_002880.4(RAF1):c.1687C>T (p.Arg563Ter)

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.1687C>T (p.Arg563Ter)
HGVS:
  • NC_000003.12:g.12584963G>A
  • NG_007467.1:g.84217C>T
  • NM_001354689.3:c.1747C>T
  • NM_001354690.3:c.1687C>T
  • NM_001354691.3:c.1444C>T
  • NM_001354692.3:c.1444C>T
  • NM_001354693.3:c.1588C>T
  • NM_001354694.3:c.1504C>T
  • NM_001354695.3:c.1345C>T
  • NM_002880.4:c.1687C>TMANE SELECT
  • NP_001341618.1:p.Arg583Ter
  • NP_001341619.1:p.Arg563Ter
  • NP_001341620.1:p.Arg482Ter
  • NP_001341621.1:p.Arg482Ter
  • NP_001341622.1:p.Arg530Ter
  • NP_001341623.1:p.Arg502Ter
  • NP_001341624.1:p.Arg449Ter
  • NP_002871.1:p.Arg563Ter
  • NP_002871.1:p.Arg563Ter
  • LRG_413t1:c.1687C>T
  • LRG_413t2:c.1747C>T
  • LRG_413:g.84217C>T
  • LRG_413p1:p.Arg563Ter
  • LRG_413p2:p.Arg583Ter
  • NC_000003.11:g.12626462G>A
  • NM_002880.3:c.1687C>T
  • NR_148940.3:n.2131C>T
  • NR_148941.3:n.2077C>T
  • NR_148942.3:n.2016C>T
Protein change:
R449*
Links:
dbSNP: rs532786413
NCBI 1000 Genomes Browser:
rs532786413
Molecular consequence:
  • NR_148940.3:n.2131C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148941.3:n.2077C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148942.3:n.2016C>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001354689.3:c.1747C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354690.3:c.1687C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354691.3:c.1444C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354692.3:c.1444C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354693.3:c.1588C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354694.3:c.1504C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001354695.3:c.1345C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_002880.4:c.1687C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
RAF1-related disorder
Synonyms:
RAF1-related disorders; RAF1-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004119530PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Aug 17, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical 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 PreventionGenetics, part of Exact Sciences, SCV004119530.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The RAF1 c.1687C>T variant is predicted to result in premature protein termination (p.Arg563*). To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Few chain-terminating variants in RAF1 are reported and loss of function has not been conclusively established as a mechanism for RAF1-related disorders. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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

Last Updated: Nov 3, 2024