rs1553259511
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_StrongPM2PP5_Very_Strong
The NM_000530.8(MPZ):c.646_647insA(p.Thr216AsnfsTer19) variant causes a frameshift, splice region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely pathogenic (★★).
Frequency
Genomes: not found (cov: 31)
Consequence
MPZ
NM_000530.8 frameshift, splice_region
NM_000530.8 frameshift, splice_region
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 1.40
Genes affected
MPZ (HGNC:7225): (myelin protein zero) This gene is specifically expressed in Schwann cells of the peripheral nervous system and encodes a type I transmembrane glycoprotein that is a major structural protein of the peripheral myelin sheath. The encoded protein contains a large hydrophobic extracellular domain and a smaller basic intracellular domain, which are essential for the formation and stabilization of the multilamellar structure of the compact myelin. Mutations in this gene are associated with autosomal dominant form of Charcot-Marie-Tooth disease type 1 (CMT1B) and other polyneuropathies, such as Dejerine-Sottas syndrome (DSS) and congenital hypomyelinating neuropathy (CHN). A recent study showed that two isoforms are produced from the same mRNA by use of alternative in-frame translation termination codons via a stop codon readthrough mechanism. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 14 ACMG points.
PVS1
Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most exon, not predicted to undergo nonsense mediated mRNA decay. There are 7 pathogenic variants in the truncated region.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 1-161305976-G-GT is Pathogenic according to our data. Variant chr1-161305976-G-GT is described in ClinVar as [Likely_pathogenic]. Clinvar id is 462798.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MPZ | NM_000530.8 | c.646_647insA | p.Thr216AsnfsTer19 | frameshift_variant, splice_region_variant | 6/6 | ENST00000533357.5 | NP_000521.2 | |
MPZ | NM_001315491.2 | c.646_647insA | p.Thr216AsnfsTer19 | frameshift_variant, splice_region_variant | 6/6 | NP_001302420.1 | ||
MPZ | XM_017001321.3 | c.675+131_675+132insA | intron_variant | XP_016856810.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
MPZ | ENST00000533357.5 | c.646_647insA | p.Thr216AsnfsTer19 | frameshift_variant, splice_region_variant | 6/6 | 1 | NM_000530.8 | ENSP00000432943 | P1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 genomes
Cov.:
31
GnomAD4 exome Cov.: 33
GnomAD4 exome
Cov.:
33
GnomAD4 genome Cov.: 31
GnomAD4 genome
Cov.:
31
ClinVar
Significance: Pathogenic/Likely pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Inborn genetic diseases Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 10, 2023 | The c.646dupA (p.T216Nfs*19) alteration, located in exon 6 (coding exon 6) of the MPZ gene, consists of a duplication of A at position 646, causing a translational frameshift with a predicted alternate stop codon after 19 amino acids. This alteration occurs at the 3' terminus of the MPZ gene, is not expected to trigger nonsense-mediated mRNA decay, and impacts the last 13% of the protein. However, premature stop codons are typically deleterious in nature, the impacted region is critical for protein function, and a significant portion of the protein is affected (Ambry internal data)._x000D_ _x000D_ _x000D_ _x000D_ for autosomal dominant MPZ-related Charcot-Marie-Tooth disease type 1 and autosomal recessive MPZ-related Dejerine-Sottas disease; however, its classification for autosomal dominant MPZ-related neuropathic disorders is uncertain. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been identified in at least one individual with clinical features of Charcot-Marie-Tooth disease (Sanmaneechai, 2015). Based on internal structural analysis, this variant results in loss of Ser233, phosphorylation of which is necessary for P0 adhesion function, and loss of a PKC substrate motif (RSTK) (Gaboreanu, 2007; Hilmi, 1995; Xu, 2001). Based on the available evidence, this alteration is classified as likely pathogenic. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 31, 2018 | - - |
Charcot-Marie-Tooth disease, type I Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 30, 2023 | This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Thr216Asnfs*19) in the MPZ gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 33 amino acid(s) of the MPZ protein. For these reasons, this variant has been classified as Pathogenic. This variant disrupts a region of the MPZ protein in which other variant(s) (p.Glu222Valfs*14) have been determined to be pathogenic (PMID: 7530550). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. ClinVar contains an entry for this variant (Variation ID: 462798). This premature translational stop signal has been observed in individuals with Charcot Marie Tooth disease (PMID: 26310628). - |
Computational scores
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at