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NM_002880.4(RAF1):c.768G>T (p.Arg256Ser) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
May 3, 2024
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:
RCV000159072.5

Allele description [Variation Report for NM_002880.4(RAF1):c.768G>T (p.Arg256Ser)]

NM_002880.4(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_002880.4(RAF1):c.768G>T (p.Arg256Ser)
Other names:
p.R256S:AGG>AGT; NM_002880.3(RAF1):c.768G>T; NM_002880.4(RAF1):c.768G>T
HGVS:
  • NC_000003.12:g.12604202C>A
  • NG_007467.1:g.64978G>T
  • NM_001354689.3:c.768G>T
  • NM_001354690.3:c.768G>T
  • NM_001354691.3:c.525G>T
  • NM_001354692.3:c.525G>T
  • NM_001354693.3:c.669G>T
  • NM_001354694.3:c.525G>T
  • NM_001354695.3:c.426G>T
  • NM_002880.4:c.768G>TMANE SELECT
  • 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
  • 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
  • NM_002880.3:c.768G>T
  • NR_148940.3:n.1099G>T
  • NR_148941.3:n.1099G>T
  • NR_148942.3: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_001354690.3:c.768G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354691.3:c.525G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354692.3:c.525G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354693.3:c.669G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354694.3:c.525G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001354695.3:c.426G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002880.4:c.768G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NR_148940.3:n.1099G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148941.3:n.1099G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_148942.3:n.1099G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000209014GeneDx
criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)		Pathogenic
(May 3, 2024) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000209014.12

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

Description

Published functional studies demonstrate a damaging effect on protein localization and activity (PMID: 20679480); Not observed in large population cohorts (gnomAD); The majority of missense variants in this gene are considered pathogenic (HGMD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 24803665, 37777071, 24957944, 9689060, 15520807, 17603483, 29493581, 19020799, 20679480)

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

Last Updated: Oct 20, 2024