VCV000656830.1 - ClinVar

NC_000017.11:g.(?_15239461)_(15260737_?)del

Germline

Classification

criteria provided, single submitter. Learn more about how ClinVar calculates review status.

Pathogenic

This classification is based on the single submission received

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NC_000017.11:g.(?_15239461)_(15260737_?)del

Variation ID: 656830 Accession: VCV000656830.1

Type and length

Deletion, 21,277 bp

Location

Cytogenetic: 17p12 17: 15239461-15260737 (GRCh38) [ NCBI UCSC ] 17: 15142778-15164054 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Aug 14, 2019	Aug 14, 2019	Sep 4, 2018

HGVS

Nucleotide	Protein	Molecular consequence
NC_000017.11:g.(?_15239461)_(15260737_?)del
NC_000017.10:g.(?_15142778)_(15164054_?)del

Protein change

Other names

Canonical SPDI

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
PMP22		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	393	490
MIR4731	-	-	-	GRCh38	-	21

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Charcot-Marie-Tooth disease, type I	Pathogenic (1)	criteria provided, single submitter	Sep 4, 2018	RCV000813337.3

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	Expand all rows Collapse all rows Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Sep 04, 2018) C Contributing to aggregate classification	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Charcot-Marie-Tooth disease, type I	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000953695.1 First in ClinVar: Aug 14, 2019 Last updated: Aug 14, 2019	Publications: PubMed (1) PubMed: 8894410 Comment: show A gross deletion of the genomic region encompassing the full coding sequence of the PMP22 gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. Approximately 80% of individuals with hereditary neuropathy with liability to pressure palsies (HNPP) have a 1.5Mb deletion at 17p11.2 (which includes PMP22) on one chromosome (PMID: 8894410,Â¬â€ 20301566). Because deletions of PMP22 are a known mechanism of disease in HNPP, this sequence change has been classified as Pathogenic. (less) Observation: 1 Collection method: clinical testing Allele origin: germline Affected status: unknown Observation 1 Collection method: clinical testing Allele origin: germline Affected status: unknown

Comment:

A gross deletion of the genomic region encompassing the full coding sequence of the PMP22 gene has been identified. The boundaries of this event are unknown as the deletion extends beyond the assayed region for this gene and therefore may encompass additional genes. Approximately 80% of individuals with hereditary neuropathy with liability to pressure palsies (HNPP) have a 1.5Mb deletion at 17p11.2 (which includes PMP22) on one chromosome (PMID: 8894410,Â¬â€ 20301566). Because deletions of PMP22 are a known mechanism of disease in HNPP, this sequence change has been classified as Pathogenic.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Deletion of the PMP22 gene and hereditary neuropathy with liability to pressure palsies.	Pareyson D	Current opinion in neurology	1996	PMID: 8894410

Text-mined citations for this variant ...

Record last updated Mar 16, 2025