1-43337858-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_005373.3(MPL):āc.10T>Cā(p.Trp4Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000048 in 1,457,286 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_005373.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MPL | ENST00000372470.9 | c.10T>C | p.Trp4Arg | missense_variant | Exon 1 of 12 | 1 | NM_005373.3 | ENSP00000361548.3 | ||
MPL | ENST00000413998.7 | c.10T>C | p.Trp4Arg | missense_variant | Exon 1 of 12 | 1 | ENSP00000414004.3 | |||
MPL | ENST00000638732.1 | n.10T>C | non_coding_transcript_exon_variant | Exon 1 of 10 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.0000165 AC: 4AN: 242964Hom.: 0 AF XY: 0.0000304 AC XY: 4AN XY: 131376
GnomAD4 exome AF: 0.00000480 AC: 7AN: 1457286Hom.: 0 Cov.: 33 AF XY: 0.00000414 AC XY: 3AN XY: 724682
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Essential thrombocythemia;C1327915:Congenital amegakaryocytic thrombocytopenia Uncertain:1
In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. This sequence change replaces tryptophan, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 4 of the MPL protein (p.Trp4Arg). This variant is present in population databases (rs752112087, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with MPL-related conditions. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on MPL protein function. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at