The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

  • See Evidence submitted by expert panel for details.

Variant: NM_001354689.3(RAF1):c.775T>G (p.Ser259Ala)

CA351512423

504514 (ClinVar)

Gene: RAF1
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: b3cd9818-3e8f-4cc2-9125-611051be63a7

HGVS expressions

NM_001354689.3:c.775T>G
NM_001354689.3(RAF1):c.775T>G (p.Ser259Ala)
NM_002880.3:c.775T>G
NM_001354689.1:c.775T>G
NM_001354690.1:c.775T>G
NM_001354691.1:c.532T>G
NM_001354692.1:c.532T>G
NM_001354693.1:c.676T>G
NM_001354694.1:c.532T>G
NM_001354695.1:c.433T>G
NR_148940.1:n.1190T>G
NR_148941.1:n.1190T>G
NR_148942.1:n.1190T>G
NM_001354690.2:c.775T>G
NM_001354691.2:c.532T>G
NM_001354692.2:c.532T>G
NM_001354693.2:c.676T>G
NM_001354694.2:c.532T>G
NM_001354695.2:c.433T>G
NR_148940.2:n.1106T>G
NR_148941.2:n.1106T>G
NR_148942.2:n.1106T>G
ENST00000251849.8:c.775T>G
ENST00000416093.1:c.*353T>G
ENST00000423275.5:c.*452T>G
ENST00000432427.2:n.412T>G
ENST00000442415.6:c.775T>G
ENST00000465826.5:n.19T>G
ENST00000491290.1:n.296T>G
NC_000003.12:g.12604195A>C
CM000665.2:g.12604195A>C
NC_000003.11:g.12645694A>C
CM000665.1:g.12645694A>C
NC_000003.10:g.12620694A>C
NG_007467.1:g.64985T>G

Pathogenic

Met criteria codes 5
PS2_Very Strong PP2 PM2 PM5_Strong PS4_Supporting
Not Met criteria codes 1
PS3

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.775T>G (p.Ser259Ala) variant in RAF1 was absent from large population studies (PM2; gnomAD, http://gnomad.broadinstitute.org). It has been reported as a confirmed de novo occurrence in 2 probands (PS2_VeryStrong; SCV000808501.1). The variant has been identified in 1 proband with Noonan syndrome (PS4_Supporting; SCV000710868.2). At least 2 other pathogenic missense variants have been previously identified at the Ser259 codon of RAF1 which may indicate that this residue is critical to the function of the protein (PM5_Strong; ClinVar 40601, 44633). A functional assay has been performed on c.775T>G (p.Ser259Ala), but given that it is not currently an approved assay outlined by the RASopathy VCEP, it has not been assessed for PS3 at this time (PMID:23391722). Finally, the variant is located in RAF1, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic missense variants are common (PP2; PMID: 29493581). Of note, this variant has also been observed in association with somatic malignancies; however, analysis and classification of somatic variation is currently not used to inform germline classifications for the RASopathies. In summary, this variant meets criteria to be classified as pathogenic for RASopathies in an autosomal dominant manner. Rasopathy-specific ACMG/AMP criteria applied (PMID:29493581): PS2_VeryStrong, PS4_Supporting, PM5_Strong, PM2, PP2.
Met criteria codes
PS2_Very Strong
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM5_Strong
S259T ClinVar ID: 40601 S259Y ClinVar ID: 44633
PS4_Supporting
1 case counted (LMM).
Not Met criteria codes
PS3
Transgenic mouse model looking at arterial morphogenesis found endothelial expression of S259A transgene leads to embryonic lethality at embryonic day (E)15.5 because of lymphatic and cardiac defects that become prominent after E14.5, whereas major arteries in the embryo proper were largely unaffected. Not an approved study to apply PS3

Approved on: 2020-06-25
Published on: 2020-06-25
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