NM_002880.4(RAF1):c.837T>A (p.Asp279Glu) AND RASopathy

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 28, 2022
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:: RCV002541380.3

Allele description [Variation Report for NM_002880.4(RAF1):c.837T>A (p.Asp279Glu)]

NM_002880.4(RAF1):c.837T>A (p.Asp279Glu)

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.837T>A (p.Asp279Glu)

HGVS:

NC_000003.12:g.12600413A>T
NG_007467.1:g.68767T>A
NM_001354689.3:c.897T>A
NM_001354690.3:c.837T>A
NM_001354691.3:c.594T>A
NM_001354692.3:c.594T>A
NM_001354693.3:c.738T>A
NM_001354694.3:c.654T>A
NM_001354695.3:c.495T>A
NM_002880.4:c.837T>AMANE SELECT
NP_001341618.1:p.Asp299Glu
NP_001341619.1:p.Asp279Glu
NP_001341620.1:p.Asp198Glu
NP_001341621.1:p.Asp198Glu
NP_001341622.1:p.Asp246Glu
NP_001341623.1:p.Asp218Glu
NP_001341624.1:p.Asp165Glu
NP_002871.1:p.Asp279Glu
LRG_413t1:c.837T>A
LRG_413t2:c.897T>A
LRG_413:g.68767T>A
LRG_413p2:p.Asp299Glu
NC_000003.11:g.12641912A>T
NM_002880.3:c.837T>A
NR_148940.3:n.1168T>A
NR_148941.3:n.1168T>A
NR_148942.3:n.1168T>A

Protein change:

D165E

Links:

dbSNP: rs2125381916

NCBI 1000 Genomes Browser:

rs2125381916

Molecular consequence:

NM_001354689.3:c.897T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354690.3:c.837T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354691.3:c.594T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354692.3:c.594T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354693.3:c.738T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354694.3:c.654T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001354695.3:c.495T>A - missense variant - [Sequence Ontology: SO:0001583]
NM_002880.4:c.837T>A - missense variant - [Sequence Ontology: SO:0001583]
NR_148940.3:n.1168T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148941.3:n.1168T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148942.3:n.1168T>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: RASopathy
Synonyms:: rasopathies; Noonan spectrum disorder
Identifiers:: MONDO: MONDO:0021060; MedGen: C5555857

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003308126	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 28, 2022)	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

SCV003308126

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 28, 2022)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003308126.2

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

Description

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1331356). This variant has not been reported in the literature in individuals affected with RAF1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces aspartic acid, which is acidic and polar, with glutamic acid, which is acidic and polar, at codon 279 of the RAF1 protein (p.Asp279Glu).

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

Last Updated: Sep 29, 2024

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