NM_002880.4(RAF1):c.785A>T (p.Asn262Ile) AND not provided

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Apr 17, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000159095.4

Allele description [Variation Report for NM_002880.4(RAF1):c.785A>T (p.Asn262Ile)]

NM_002880.4(RAF1):c.785A>T (p.Asn262Ile)

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.785A>T (p.Asn262Ile)

Other names:

p.N262I:AAT>ATT

HGVS:

NC_000003.12:g.12604185T>A
NG_007467.1:g.64995A>T
NM_001354689.3:c.785A>T
NM_001354690.3:c.785A>T
NM_001354691.3:c.542A>T
NM_001354692.3:c.542A>T
NM_001354693.3:c.686A>T
NM_001354694.3:c.542A>T
NM_001354695.3:c.443A>T
NM_002880.4:c.785A>TMANE SELECT
NP_001341618.1:p.Asn262Ile
NP_001341619.1:p.Asn262Ile
NP_001341620.1:p.Asn181Ile
NP_001341621.1:p.Asn181Ile
NP_001341622.1:p.Asn229Ile
NP_001341623.1:p.Asn181Ile
NP_001341624.1:p.Asn148Ile
NP_002871.1:p.Asn262Ile
NP_002871.1:p.Asn262Ile
LRG_413t1:c.785A>T
LRG_413t2:c.785A>T
LRG_413:g.64995A>T
LRG_413p1:p.Asn262Ile
LRG_413p2:p.Asn262Ile
NC_000003.11:g.12645684T>A
NM_002880.3:c.785A>T
NR_148940.3:n.1116A>T
NR_148941.3:n.1116A>T
NR_148942.3:n.1116A>T

Protein change:

N148I

Links:

dbSNP: rs730881010

NCBI 1000 Genomes Browser:

rs730881010

Molecular consequence:

NM_001354689.3:c.785A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354690.3:c.785A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354691.3:c.542A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354692.3:c.542A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354693.3:c.686A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354694.3:c.542A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001354695.3:c.443A>T - missense variant - [Sequence Ontology: SO:0001583]
NM_002880.4:c.785A>T - missense variant - [Sequence Ontology: SO:0001583]
NR_148940.3:n.1116A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148941.3:n.1116A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148942.3:n.1116A>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: none provided; RECLASSIFIED - ADRA2C POLYMORPHISM; RECLASSIFIED - ADRB1 POLYMORPHISM
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000209038	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Apr 17, 2023)	germline	clinical testing	Citation Link,
SCV000927370	Blueprint Genetics	criteria provided, single submitter (Blueprint Genetics Variant Classification Scheme)	Likely pathogenic (Aug 9, 2017)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000209038

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Apr 17, 2023)

germline

clinical testing

Citation Link,

SCV000927370

Blueprint Genetics

criteria provided, single submitter

(Blueprint Genetics Variant Classification Scheme)

Likely pathogenic
(Aug 9, 2017)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From GeneDx, SCV000209038.10

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Missense variants in this gene are often considered pathogenic (HGMD); This variant is associated with the following publications: (PMID: 24451042, 24957944, 9689060, 15520807, 17603483, 17603482, 29493581, 19020799)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Blueprint Genetics, SCV000927370.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Feb 25, 2025

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