NM_002880.4(RAF1):c.1688G>A (p.Arg563Gln) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Mar 6, 2014
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:: RCV000156167.5

Allele description [Variation Report for NM_002880.4(RAF1):c.1688G>A (p.Arg563Gln)]

NM_002880.4(RAF1):c.1688G>A (p.Arg563Gln)

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.1688G>A (p.Arg563Gln)

HGVS:

NC_000003.12:g.12584962C>T
NG_007467.1:g.84218G>A
NM_001354689.3:c.1748G>A
NM_001354690.3:c.1688G>A
NM_001354691.3:c.1445G>A
NM_001354692.3:c.1445G>A
NM_001354693.3:c.1589G>A
NM_001354694.3:c.1505G>A
NM_001354695.3:c.1346G>A
NM_002880.4:c.1688G>AMANE SELECT
NP_001341618.1:p.Arg583Gln
NP_001341619.1:p.Arg563Gln
NP_001341620.1:p.Arg482Gln
NP_001341621.1:p.Arg482Gln
NP_001341622.1:p.Arg530Gln
NP_001341623.1:p.Arg502Gln
NP_001341624.1:p.Arg449Gln
NP_002871.1:p.Arg563Gln
NP_002871.1:p.Arg563Gln
LRG_413t1:c.1688G>A
LRG_413t2:c.1748G>A
LRG_413:g.84218G>A
LRG_413p1:p.Arg563Gln
LRG_413p2:p.Arg583Gln
NC_000003.11:g.12626461C>T
NM_002880.3:c.1688G>A
NR_148940.3:n.2132G>A
NR_148941.3:n.2078G>A
NR_148942.3:n.2017G>A

Protein change:

R449Q

Links:

dbSNP: rs727504827

NCBI 1000 Genomes Browser:

rs727504827

Molecular consequence:

NM_001354689.3:c.1748G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354690.3:c.1688G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354691.3:c.1445G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354692.3:c.1445G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354693.3:c.1589G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354694.3:c.1505G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354695.3:c.1346G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002880.4:c.1688G>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148940.3:n.2132G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148941.3:n.2078G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148942.3:n.2017G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

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DNA damage-inducible transcript 3 protein isoform 2 [Homo sapiens]
DNA damage-inducible transcript 3 protein isoform 2 [Homo sapiens]
gi|21361118|ref|NP_004074.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000205883	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Uncertain significance (Mar 6, 2014)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000205883

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Uncertain significance
(Mar 6, 2014)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	2	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000205883.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	PubMed (1)

Description

The Arg563Gln variant in SOS1 has now been identified by our laboratory in one a ffected individual and his reportedly unaffected mother. Computational predictio n tools and conservation analyses do not provide strong support for or against a n impact to the normal function of the protein. In summary, additional informati on is needed to assess the clinical significance of the Arg563Gln variant.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		2	not provided	1	not provided

Last Updated: Sep 29, 2024

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