rs878854029
Variant summary
Our verdict is Uncertain significance. Variant got 5 ACMG points: 5P and 0B. PVS1_ModeratePM2PP5
The NM_001195798.2(LDLR):c.2548-3_2548delCAGA(p.Met850fs) variant causes a frameshift, splice acceptor, splice region, intron change. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001195798.2 frameshift, splice_acceptor, splice_region, intron
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LDLR | NM_000527.5 | c.2551_2554delCAGA | p.Gln851fs | frameshift_variant | Exon 18 of 18 | ENST00000558518.6 | NP_000518.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Familial hypercholesterolemia Pathogenic:1
This sequence change results in a frameshift in the LDLR gene (p.Gln851Trpfs*77). While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 10 amino acid(s) of the LDLR protein and extend the protein by 66 additional amino acid residues. This variant is not present in population databases (gnomAD no frequency). This frameshift has been observed in individuals with clinical features of familial hypercholesterolemia (internal data). Invitae Evidence Modeling of clinical and family history, age, sex, and reported ancestry of multiple individuals with this LDLR variant has been performed. This variant is expected to be pathogenic with a positive predictive value of at least 99%. This is a validated machine learning model that incorporates the clinical features of 363,995 individuals referred to our laboratory for LDLR testing. ClinVar contains an entry for this variant (Variation ID: 237871). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic. -
Hypercholesterolemia, familial, 1 Uncertain:1
This sequence change deletes 4 nucleotides from exon 18 of the LDLR mRNA (c.2551_2554delCAGA), causing a frameshift at codon 851. This leads to the substitution of the last 10 amino acids of the LDLR protein with 77 unrelated amino acids (p.Gln851Trpfs*77). While this is not anticipated to result in nonsense mediated decay, it is expected to result in a LDLR protein with an aberrant C-terminus. Truncating sequence changes in the last exon of LDLR are not necessarily pathogenic.This particular frameshift variant has not been reported in the literature and there are no proven pathogenic variants reported in this exon. In summary, this is a novel frameshift variant with uncertain impact on protein function. It has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at