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NM_001042432.2(CLN3):c.1059C>A (p.Cys353Ter) AND Neuronal ceroid lipofuscinosis

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Jan 7, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000989587.3

Allele description [Variation Report for NM_001042432.2(CLN3):c.1059C>A (p.Cys353Ter)]

NM_001042432.2(CLN3):c.1059C>A (p.Cys353Ter)

Gene:
CLN3:CLN3 lysosomal/endosomal transmembrane protein, battenin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p12.1
Genomic location:
Preferred name:
NM_001042432.2(CLN3):c.1059C>A (p.Cys353Ter)
HGVS:
  • NC_000016.10:g.28477875G>T
  • NG_008654.2:g.19428C>A
  • NM_000086.2:c.1059C>A
  • NM_001042432.2:c.1059C>AMANE SELECT
  • NM_001286104.2:c.987C>A
  • NM_001286105.2:c.759C>A
  • NM_001286109.2:c.825C>A
  • NM_001286110.2:c.897C>A
  • NP_000077.1:p.Cys353Ter
  • NP_001035897.1:p.Cys353Ter
  • NP_001035897.1:p.Cys353Ter
  • NP_001273033.1:p.Cys329Ter
  • NP_001273034.1:p.Cys253Ter
  • NP_001273038.1:p.Cys275Ter
  • NP_001273039.1:p.Cys299Ter
  • LRG_689t1:c.1059C>A
  • LRG_689t2:c.1059C>A
  • LRG_689:g.19428C>A
  • LRG_689p1:p.Cys353Ter
  • LRG_689p2:p.Cys353Ter
  • NC_000016.9:g.28489196G>T
  • NM_001042432.1:c.1059C>A
Protein change:
C253*
Links:
dbSNP: rs1057516677
NCBI 1000 Genomes Browser:
rs1057516677
Molecular consequence:
  • NM_000086.2:c.1059C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001042432.2:c.1059C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001286104.2:c.987C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001286105.2:c.759C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001286109.2:c.825C>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001286110.2:c.897C>A - nonsense - [Sequence Ontology: SO:0001587]

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

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001140077Mendelics
criteria provided, single submitter

(Mendelics Assertion Criteria 2017)
Pathogenic
(May 28, 2019)
unknownclinical testing

Citation Link,

SCV004426240Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 7, 2023)
germlineclinical testing

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

Summary from all submissions

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

Citations

PubMed

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

Detailed Clinical Phenotype and Molecular Genetic Findings in CLN3-Associated Isolated Retinal Degeneration.

Ku CA, Hull S, Arno G, Vincent A, Carss K, Kayton R, Weeks D, Anderson GW, Geraets R, Parker C, Pearce DA, Michaelides M, MacLaren RE, Robson AG, Holder GE, Heon E, Raymond FL, Moore AT, Webster AR, Pennesi ME.

JAMA Ophthalmol. 2017 Jul 1;135(7):749-760. doi: 10.1001/jamaophthalmol.2017.1401.

PubMed [citation]
PMID:
28542676
PMCID:
PMC5710208
See all PubMed Citations (3)

Details of each submission

From Mendelics, SCV001140077.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1unknownunknownnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004426240.1

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

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. ClinVar contains an entry for this variant (Variation ID: 370675). This variant has not been reported in the literature in individuals affected with CLN3-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Cys353*) 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