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NM_001354689.3(RAF1):c.779C>A (p.Thr260Lys)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Feb 21, 2021)
Last evaluated:
Jul 21, 2020
Accession:
VCV000639302.4
Variation ID:
639302
Description:
single nucleotide variant
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NM_001354689.3(RAF1):c.779C>A (p.Thr260Lys)

Allele ID
630886
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
3p25.2
Genomic location
3: 12604191 (GRCh38) GRCh38 UCSC
3: 12645690 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000003.11:g.12645690G>T
NC_000003.12:g.12604191G>T
NG_007467.1:g.64989C>A
... more HGVS
Protein change
T146K, T179K, T260K, T227K
Other names
-
Canonical SPDI
NC_000003.12:12604190:G:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
dbSNP: rs869025501
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 2 criteria provided, multiple submitters, no conflicts Jul 8, 2020 RCV000792062.1
Pathogenic 1 criteria provided, single submitter Jul 21, 2020 RCV001330997.1
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
RAF1 No evidence available No evidence available GRCh38
GRCh37
566 619

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Aug 16, 2018)
criteria provided, single submitter
Method: clinical testing
Rasopathy
Allele origin: germline
Invitae
Accession: SCV000931334.1
Submitted: (Mar 28, 2019)
Evidence details
Comment:
This sequence change replaces threonine with lysine at codon 260 of the RAF1 protein (p.Thr260Lys). The threonine residue is highly conserved and there is a … (more)
Likely pathogenic
(Jul 08, 2020)
criteria provided, single submitter
Method: clinical testing
Rasopathy
(Autosomal dominant inheritance)
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001361778.1
Submitted: (Jul 14, 2020)
Evidence details
Comment:
Variant summary: RAF1 c.779C>A (p.Thr260Lys) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging … (more)
Pathogenic
(Jul 21, 2020)
criteria provided, single submitter
Method: clinical testing
Noonan syndrome 5
Allele origin: de novo
Baylor Genetics
Accession: SCV001522880.1
Submitted: (Feb 21, 2021)
Evidence details
Comment:
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs869025501...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 08, 2021