rs1060503423
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PM1PM2PM5PP3_StrongPP5_Very_Strong
The NM_000530.8(MPZ):c.301T>C(p.Trp101Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W101C) has been classified as Likely pathogenic.
Frequency
Consequence
NM_000530.8 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MPZ | NM_000530.8 | c.301T>C | p.Trp101Arg | missense_variant | 3/6 | ENST00000533357.5 | |
MPZ | NM_001315491.2 | c.301T>C | p.Trp101Arg | missense_variant | 3/6 | ||
MPZ | XM_017001321.3 | c.331T>C | p.Trp111Arg | missense_variant | 3/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MPZ | ENST00000533357.5 | c.301T>C | p.Trp101Arg | missense_variant | 3/6 | 1 | NM_000530.8 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 29
GnomAD4 exome Cov.: 34
GnomAD4 genome ? Cov.: 29
ClinVar
Submissions by phenotype
Charcot-Marie-Tooth disease type 1B Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Charcot-Marie-Tooth disease, type I Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Invitae | Dec 15, 2019 | This variant disrupts the p.Trp101 amino acid residue in MPZ. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 7550231). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. 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) performed at Invitae indicates that this missense variant is expected to disrupt MPZ protein function. This variant has been observed in individual(s) with clinical features of Charcot-Marie-Tooth disease (Invitae). ClinVar contains an entry for this variant (Variation ID: 411674). This variant is not present in population databases (ExAC no frequency). This sequence change replaces tryptophan with arginine at codon 101 of the MPZ protein (p.Trp101Arg). The tryptophan residue is highly conserved and there is a moderate physicochemical difference between tryptophan and arginine. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at