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NC_000013.11:g.(?_76995053)_(76995238_?)dup AND Neuronal ceroid lipofuscinosis

Germline classification:
Likely pathogenic (1 submission)
Last evaluated:
Sep 28, 2019
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:
RCV001033119.3

Allele description

NC_000013.11:g.(?_76995053)_(76995238_?)dup

Gene:
CLN5:CLN5 intracellular trafficking protein [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
13q22.3
Genomic location:
Chr13: 77569188 - 77569373 (on Assembly GRCh37)
Preferred name:
NC_000013.11:g.(?_76995053)_(76995238_?)dup
HGVS:
  • NC_000013.11:g.(?_76995053)_(76995238_?)dup
  • NC_000013.10:g.(?_77569188)_(77569373_?)dup

Condition(s)

Name:
Neuronal ceroid lipofuscinosis
Synonyms:
Ceroid storage disease
Identifiers:
MONDO: MONDO:0016295; MedGen: C0027877; Orphanet: 79263; OMIM: PS256730

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001196426Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Likely pathogenic
(Sep 28, 2019) 		germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Next-generation sequencing of duplication CNVs reveals that most are tandem and some create fusion genes at breakpoints.

Newman S, Hermetz KE, Weckselblatt B, Rudd MK.

Am J Hum Genet. 2015 Feb 5;96(2):208-20. doi: 10.1016/j.ajhg.2014.12.017. Epub 2015 Jan 29.

PubMed [citation]
PMID:
25640679
PMCID:
PMC4320257

CLN5 mutations are frequent in juvenile and late-onset non-Finnish patients with NCL.

Xin W, Mullen TE, Kiely R, Min J, Feng X, Cao Y, O'Malley L, Shen Y, Chu-Shore C, Mole SE, Goebel HH, Sims K.

Neurology. 2010 Feb 16;74(7):565-71. doi: 10.1212/WNL.0b013e3181cff70d.

PubMed [citation]
PMID:
20157158
See all PubMed Citations (3)

Details of each submission

From Invitae, SCV001196426.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This variant results in a copy number gain of the genomic region encompassing exon 2 of the CLN5 gene. While the exact position of this variant cannot be determined from this data, sub-genic copy number gains are generally in tandem (PMID: 25640679) and may result in an absent or disrupted protein product. This variant has not been reported in the literature in individuals with CLN5-related conditions. Loss-of-function variants in CLN5 are known to be pathogenic (PMID: 20157158). 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.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 13, 2023