NM_002880.4(RAF1):c.1673T>C (p.Ile558Thr) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 11, 2018
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:: RCV000781807.1

Allele description [Variation Report for NM_002880.4(RAF1):c.1673T>C (p.Ile558Thr)]

NM_002880.4(RAF1):c.1673T>C (p.Ile558Thr)

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.1673T>C (p.Ile558Thr)

HGVS:

NC_000003.12:g.12584977A>G
NG_007467.1:g.84203T>C
NM_001354689.3:c.1733T>C
NM_001354690.3:c.1673T>C
NM_001354691.3:c.1430T>C
NM_001354692.3:c.1430T>C
NM_001354693.3:c.1574T>C
NM_001354694.3:c.1490T>C
NM_001354695.3:c.1331T>C
NM_002880.4:c.1673T>CMANE SELECT
NP_001341618.1:p.Ile578Thr
NP_001341619.1:p.Ile558Thr
NP_001341620.1:p.Ile477Thr
NP_001341621.1:p.Ile477Thr
NP_001341622.1:p.Ile525Thr
NP_001341623.1:p.Ile497Thr
NP_001341624.1:p.Ile444Thr
NP_002871.1:p.Ile558Thr
NP_002871.1:p.Ile558Thr
LRG_413t1:c.1673T>C
LRG_413t2:c.1733T>C
LRG_413:g.84203T>C
LRG_413p1:p.Ile558Thr
LRG_413p2:p.Ile578Thr
NC_000003.11:g.12626476A>G
NM_002880.3:c.1673T>C
NR_148940.3:n.2117T>C
NR_148941.3:n.2063T>C
NR_148942.3:n.2002T>C

Protein change:

I444T

Links:

dbSNP: rs1559399152

NCBI 1000 Genomes Browser:

rs1559399152

Molecular consequence:

NM_001354689.3:c.1733T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354690.3:c.1673T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354691.3:c.1430T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354692.3:c.1430T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354693.3:c.1574T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354694.3:c.1490T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001354695.3:c.1331T>C - missense variant - [Sequence Ontology: SO:0001583]
NM_002880.4:c.1673T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_148940.3:n.2117T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148941.3:n.2063T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_148942.3:n.2002T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000920141	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Uncertain significance (Jan 11, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000920141

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Uncertain significance
(Jan 11, 2018)

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

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000920141.1

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

Description

Variant summary: The c.1673T>C (p.Ile558Thr) is a missense variant that involves a conserved nucleotide and 5/5 in silico tools predict deleterious outcome. The variant is located within the catalytic domain, however impact of this change on the protein function has yet to be studied. This variant is absent from the control population dataset of ExAC (0/~246042 chromosomes), suggesting this variant is not a common polymorphism. The variant has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical laboratories. Because of the absence of clinical information and lack of functional studies, the variant was classified as a variant of uncertain significance (VUS) until additional information becomes available.

#	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: Apr 23, 2022

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