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_002880.3(RAF1):c.779C>T (p.Thr260Ile)

CA351736

222774 (ClinVar)

Gene: RAF1
Condition: RASopathy
Inheritance Mode: Autosomal dominant inheritance
UUID: d61ef783-d3ed-4577-9f3c-3f2b6c65e7be
Approved on: 2020-03-09
Published on: 2020-03-09

HGVS expressions

NM_002880.3:c.779C>T
NM_002880.3(RAF1):c.779C>T (p.Thr260Ile)
NC_000003.12:g.12604191G>A
CM000665.2:g.12604191G>A
NC_000003.11:g.12645690G>A
CM000665.1:g.12645690G>A
NC_000003.10:g.12620690G>A
NG_007467.1:g.64989C>T
NM_001354689.1:c.779C>T
NM_001354690.1:c.779C>T
NM_001354691.1:c.536C>T
NM_001354692.1:c.536C>T
NM_001354693.1:c.680C>T
NM_001354694.1:c.536C>T
NM_001354695.1:c.437C>T
NR_148940.1:n.1194C>T
NR_148941.1:n.1194C>T
NR_148942.1:n.1194C>T
NM_001354689.3:c.779C>T
NM_001354690.2:c.779C>T
NM_001354691.2:c.536C>T
NM_001354692.2:c.536C>T
NM_001354693.2:c.680C>T
NM_001354694.2:c.536C>T
NM_001354695.2:c.437C>T
NR_148940.2:n.1110C>T
NR_148941.2:n.1110C>T
NR_148942.2:n.1110C>T
ENST00000251849.8:c.779C>T
ENST00000416093.1:c.*357C>T
ENST00000423275.5:c.*456C>T
ENST00000432427.2:n.416C>T
ENST00000442415.6:c.779C>T
ENST00000465826.5:n.23C>T
ENST00000491290.1:n.300C>T
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Uncertain Significance

The Expert Panel has overridden the computationally generated classification - "Likely Pathogenic"
Met criteria codes 4
PM1 PM2 PS3 PP2
Not Met criteria codes 3
PM5 PS4 PP3

Evidence Links 1

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
RASopathy VCEP
The c.779C>T (p.Thr260Ile) variant in RAF1 was absent from large population databases (PM2; gnomad.broadinstitute.org). It occurs in the CR2 domain of the protein, which has been identified as a region important for protein function (PM1, 29493581). In vitro functional assays indicate that this variant may impact protein function (PS3; PMID: 20679480). The variant is located in the RAF1 gene, which has been defined by the ClinGen RASopathy Expert Panel as a gene with a low rate of benign missense variants and pathogenic variants are common (PP2; PMID: 29493581). Computational prediction tools and conservation analyses do not provide strong support for or against an impact to the protein. This variant has been observed in multiple probands who lacked consistent RASopathy phenotypes; however, many probands presented with cardiomyopathy (PMID: 17603483; Blueprint Genetics internal data, SCV000264163.2; Invitae internal data, SCV000824563.1; Ambry internal data, SCV000740058.2; GeneDx internal data, SCV000582743.4). Although criteria suggest that this variant is likely pathogenic given its location and in vitro functional studies, the lack of clear clinical presentations of a RASopathy phenotype supports that this variant is of uncertain significance at this time. RASopathy-specific ACMG/AMP criteria applied: PS3, PM1, PM2, PP2.
Met criteria codes
PM1
Occurs in the CR2 domain [aa 251-266/ex7].
PM2
Absent from gnomAD v2 and v3.
PS3
Kinase activity assay from Molzan et al. 2010 (PMID: 20679480) demonstrated increased phosphorylation of ERK compared to WT.

PP2
RAF1 is a missense-constrained gene.
Not Met criteria codes
PM5
Not applied since PM1 is already met. 2 variants in this codon are reported in ClinVar, but neither have been evaluated by the VCEP and have only 1 submitter each.
PS4
One case from Invitae had short stature and a broad neck, but no diagnosis of a RASopathy (SCV000824563.1). Other cases had only HCM (PMID: 17603483; GeneDx internal data, SCV000582743.4; Ambry internal data, SCV000740058.2; Blueprint internal data, SCV000264163.2).
PP3
REVEL score 0.623. Highly conserved (no animals in UCSC database have Ile at this position). Splicing is not predicted to be impacted.
Curation History
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