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NM_006493.4(CLN5):c.566_*1548del (p.Gly189fs) AND Neuronal ceroid lipofuscinosis

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jun 5, 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:
RCV000700461.3

Allele description [Variation Report for NM_006493.4(CLN5):c.566_*1548del (p.Gly189fs)]

NM_006493.4(CLN5):c.566_*1548del (p.Gly189fs)

Gene:
CLN5:CLN5 intracellular trafficking protein [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
13q22.3
Genomic location:
Preferred name:
NM_006493.4(CLN5):c.566_*1548del (p.Gly189fs)
HGVS:
  • NC_000013.11:g.77000458_77002517del
  • NG_009064.1:g.13535_15594del
  • NM_001366624.2:c.*15_*2074del
  • NM_006493.4:c.566_*1548delMANE SELECT
  • NP_006484.2:p.Gly189fs
  • LRG_692t1:c.713_*1548del
  • LRG_692:g.13535_15594del
  • NC_000013.10:g.77574593_77576652del
  • NM_006493.2:c.713_*1548del
Protein change:
G189fs
Molecular consequence:
  • NM_001366624.2:c.*15_*2074del - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_006493.4:c.566_*1548del - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000829218Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jun 5, 2018) 		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

CLN5, a novel gene encoding a putative transmembrane protein mutated in Finnish variant late infantile neuronal ceroid lipofuscinosis.

Savukoski M, Klockars T, Holmberg V, Santavuori P, Lander ES, Peltonen L.

Nat Genet. 1998 Jul;19(3):286-8.

PubMed [citation]
PMID:
9662406

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV000829218.1

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

Description

This variant is a gross deletion of the genomic region encompassing part of exon 4 of the CLN5 gene. The 5' boundary is located at c.752 (p.Asp251). The 3' end of this event is unknown as it extends through the termination codon beyond the assayed region for this gene and may encompass additional genes. While this deletion is not anticipated to result in nonsense mediated decay, it is expected to create a truncated protein product or disrupt mRNA translation. A similar deletion encompassing  a large portion of exon 4 has been reported in combination with other CLN5 alleles in individuals with neuronal ceroid lipofuscinosis (PMID: 20157158). A different truncation (p.Tyr392*) that lies downstream of this variant has been determined to be pathogenic (PMID: 9662406, Invitae). This suggests that deletion of this region of the CLN5 protein is causative of disease. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024