chr17-15239509-CC-A

Position:

• chr17-15239509-CC-A

Variant summary

Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1 PM2 PP5_Moderate

The NM_000304.4(PMP22):​c.280_281delGGinsT​(p.Gly94fs) variant causes a frameshift, missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★).

• Frequency: Genomes: not found (cov: 33)
• Consequence: PMP22 NM_000304.4 frameshift, missense
• Clinical Significance: Pathogenic criteria provided, single submitter P:1
• Conservation: PhyloP100: 7.74

Genes affected

PMP22 (HGNC:9118): (peripheral myelin protein 22) This gene encodes an integral membrane protein that is a major component of myelin in the peripheral nervous system. Studies suggest two alternately used promoters drive tissue-specific expression. Various mutations of this gene are causes of Charcot-Marie-Tooth disease Type IA, Dejerine-Sottas syndrome, and hereditary neuropathy with liability to pressure palsies. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]

PMP22 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 12 ACMG points.

• PVS1: Loss of function variant, product does not undergo nonsense mediated mRNA decay. Variant is located in the 3'-most 50 bp of the penultimate exon, not predicted to undergo nonsense mediated mRNA decay. There are 27 pathogenic variants in the truncated region.
• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 17-15239509-CC-A is Pathogenic according to our data. Variant chr17-15239509-CC-A is described in ClinVar as [Pathogenic]. Clinvar id is 220861.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PMP22	NM_000304.4	c.280_281delGGinsT	p.Gly94fs	frameshift_variant, missense_variant	4/5	ENST00000312280.9	NP_000295.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PMP22	ENST00000312280.9	c.280_281delGGinsT	p.Gly94fs	frameshift_variant, missense_variant	4/5	1	NM_000304.4	ENSP00000308937.3

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: criteria provided, single submitter

Submissions by phenotype

Charcot-Marie-Tooth disease, type I Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 21, 2015

This sequence change deletes 2 nucleotides and inserts 1 nucleotide in exon 4 of the PMP22 mRNA (c.280_281delinsT), causing a frameshift at codon 94. This creates a premature translational stop signal in the last exon of the PMP22 mRNA (p.Gly94Serfs*17). While this is not anticipated to result in nonsense mediated decay, it is expected to result in a truncated PMP22 protein. This variant is not present in population databases (ExAC no frequency) and has not been reported in the literature. This variant has been observed to occur de novo in an affected individual tested at Invitae. In addition, a different variant (NM_000304.3:c.281delG) giving rise to a very similar protein effect  (p.Gly94Alafs*17) has been reported in several patients affected with CMT and Dejerine−Sottas syndrome (PMID: 9324088, 11545686, 11835375, 19067730, 26392352), which also suggests that the sequence change observed here is disease-causing. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs864622678; hg19: chr17-15142826;