NM_000271.5(NPC1):c.3243_3755-94del AND Niemann-Pick disease, type C

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Feb 2, 2018
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV000781672.1

Allele description [Variation Report for NM_000271.5(NPC1):c.3243_3755-94del]

NM_000271.5(NPC1):c.3243_3755-94del

Gene:

NPC1:NPC intracellular cholesterol transporter 1 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

18q11.2

Genomic location:

Preferred name:

NM_000271.5(NPC1):c.3243_3755-94del

HGVS:

NC_000018.10:g.23532378_23536675del
NG_012795.1:g.54943_59240del
NG_033119.1:g.33909_35338del
NM_000271.5:c.3243_3755-94delMANE SELECT
NC_000018.9:g.21112342_21116639del
NM_000271.4:c.3243_3755-94del

Molecular consequence:

NM_000271.5:c.3243_3755-94del - splice acceptor variant - [Sequence Ontology: SO:0001574]
NM_000271.5:c.3243_3755-94del - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: Niemann-Pick disease, type C (NPC)
Identifiers:: MONDO: MONDO:0018982; MedGen: C0220756

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000919896	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015)	Likely pathogenic (Feb 2, 2018)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000919896

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

criteria provided, single submitter

(LabCorp Variant Classification Summary - May 2015)

Likely pathogenic
(Feb 2, 2018)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Details of each submission

From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV000919896.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Variant summary: NPC1 c.3243_3755-94del is a large deletion spanning exons 21-24 in the NPC1 gene, which results in a frameshift change in the NPC1 gene, a known mechanism of disease. The frequency of this variant in the general population could not be determined as the technology used for large population databases (ExAC, gnomAD, ESP, 1000G) cannot detect variants of this type. To our knowledge, no occurrence of c.3243_3755-94del in individuals affected with Niemann-Pick Disease Type C and no experimental evidence demonstrating its impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Based on the evidence outlined above, the variant was classified as likely pathogenic.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Mar 30, 2024

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