rs1555610854
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The ENST00000358273.9(NF1):c.909_910delinsTT(p.Arg304Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. L303L) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 32)
Consequence
NF1
ENST00000358273.9 stop_gained
ENST00000358273.9 stop_gained
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.69
Genes affected
NF1 (HGNC:7765): (neurofibromin 1) This gene product appears to function as a negative regulator of the ras signal transduction pathway. Mutations in this gene have been linked to neurofibromatosis type 1, juvenile myelomonocytic leukemia and Watson syndrome. The mRNA for this gene is subject to RNA editing (CGA>UGA->Arg1306Term) resulting in premature translation termination. Alternatively spliced transcript variants encoding different isoforms have also been described for this gene. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 17-31200442-AC-TT is Pathogenic according to our data. Variant chr17-31200442-AC-TT is described in ClinVar as [Pathogenic]. Clinvar id is 527594.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NF1 | NM_001042492.3 | c.909_910delinsTT | p.Arg304Ter | stop_gained | 9/58 | ENST00000358273.9 | NP_001035957.1 | |
NF1 | NM_000267.3 | c.909_910delinsTT | p.Arg304Ter | stop_gained | 9/57 | NP_000258.1 | ||
NF1 | NM_001128147.3 | c.909_910delinsTT | p.Arg304Ter | stop_gained | 9/15 | NP_001121619.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NF1 | ENST00000358273.9 | c.909_910delinsTT | p.Arg304Ter | stop_gained | 9/58 | 1 | NM_001042492.3 | ENSP00000351015 | P1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Neurofibromatosis, type 1 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 10, 2017 | For these reasons, this variant has been classified as Pathogenic. Loss-of-function variants in NF1 are known to be pathogenic (PMID: 10712197, 23913538). Experimental studies for the c.910C>T variant have shown that, instead of creating a truncated protein, it causes skipping of exon 9 (also known as exon 7 in the literature). This creates a smaller transcript that lacks these codons and is expressed at a decreased amount when compared to wild-type transcript (PMID: 9463322, 10874316). Experimental studies are not available for the c.909_910delACinsTT variant and it is unclear if it will also result in a similar disruption to mRNA splicing. However, either way, it is expected to result in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with NF1-related disease. However, a different variant (c.910C>T) giving rise to the same protein effect observed here (p.Arg304*) has been reported in many individuals affected with neurofibromatosis, type 1 (PMID: 23668869, 16786508, 23913538, 10862084) and has been determined to be Pathogenic. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Arg304*) in the NF1 gene. It is expected to result in an absent or disrupted protein product. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at