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NM_001042432.2(CLN3):c.1048del (p.Leu350fs) AND Neuronal ceroid lipofuscinosis

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jan 28, 2023
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:
RCV001853040.4

Allele description [Variation Report for NM_001042432.2(CLN3):c.1048del (p.Leu350fs)]

NM_001042432.2(CLN3):c.1048del (p.Leu350fs)

Gene:
CLN3:CLN3 lysosomal/endosomal transmembrane protein, battenin [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
16p12.1
Genomic location:
Preferred name:
NM_001042432.2(CLN3):c.1048del (p.Leu350fs)
HGVS:
  • NC_000016.10:g.28482115del
  • NG_008654.2:g.15190del
  • NM_000086.2:c.1048del
  • NM_001042432.2:c.1048delMANE SELECT
  • NM_001286104.2:c.976del
  • NM_001286105.2:c.748del
  • NM_001286109.2:c.814del
  • NM_001286110.2:c.886del
  • NP_000077.1:p.Leu350fs
  • NP_001035897.1:p.Leu350fs
  • NP_001273033.1:p.Leu326fs
  • NP_001273034.1:p.Leu250fs
  • NP_001273038.1:p.Leu272fs
  • NP_001273039.1:p.Leu296fs
  • LRG_689t1:c.1048del
  • LRG_689:g.15190del
  • LRG_689p1:p.Leu350fs
  • NC_000016.9:g.28493434del
  • NC_000016.9:g.28493436del
  • NM_001042432.1:c.1048delC
Protein change:
L250fs
Links:
dbSNP: rs386833696
NCBI 1000 Genomes Browser:
rs386833696
Molecular consequence:
  • NM_000086.2:c.1048del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001042432.2:c.1048del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001286104.2:c.976del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001286105.2:c.748del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001286109.2:c.814del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001286110.2:c.886del - 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
SCV002232676Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Jan 28, 2023) 		germlineclinical testing

PubMed (4)
[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

Update of the mutation spectrum and clinical correlations of over 360 mutations in eight genes that underlie the neuronal ceroid lipofuscinoses.

Kousi M, Lehesjoki AE, Mole SE.

Hum Mutat. 2012 Jan;33(1):42-63. doi: 10.1002/humu.21624. Epub 2011 Nov 16. Review.

PubMed [citation]
PMID:
21990111

Spectrum of mutations in the Batten disease gene, CLN3.

Munroe PB, Mitchison HM, O'Rawe AM, Anderson JW, Boustany RM, Lerner TJ, Taschner PE, de Vos N, Breuning MH, Gardiner RM, Mole SE.

Am J Hum Genet. 1997 Aug;61(2):310-6.

PubMed [citation]
PMID:
9311735
PMCID:
PMC1715900
See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002232676.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. ClinVar contains an entry for this variant (Variation ID: 56245). This premature translational stop signal has been observed in individual(s) with CLN3-related conditions (PMID: 21990111). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Leu350Cysfs*27) in the CLN3 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CLN3 are known to be pathogenic (PMID: 9311735, 28542676).

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

Last Updated: Sep 29, 2024