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NM_001042432.2(CLN3):c.883G>T (p.Glu295Ter)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Oct 12, 2021)
Last evaluated:
Aug 10, 2021
Accession:
VCV000056290.7
Variation ID:
56290
Description:
single nucleotide variant
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NM_001042432.2(CLN3):c.883G>T (p.Glu295Ter)

Allele ID
70929
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16p12.1
Genomic location
16: 28482500 (GRCh38) GRCh38 UCSC
16: 28493821 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.9:g.28493821C>A
NM_001042432.1:c.883G>T NP_001035897.1:p.Glu295Ter nonsense
LRG_689:g.14803G>T
... more HGVS
Protein change
E295*, E241*, E271*, E195*, E217*
Other names
-
Canonical SPDI
NC_000016.10:28482499:C:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (T)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
ClinGen: CA263730
dbSNP: rs121434286
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Aug 10, 2021 RCV000049702.2
Pathogenic 2 criteria provided, multiple submitters, no conflicts Mar 11, 2021 RCV001055217.3
Pathogenic 1 criteria provided, single submitter Oct 8, 2020 RCV001552759.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CLN3 - - GRCh38
GRCh37
617 681

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Jul 27, 2017)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 3
Allele origin: unknown
Counsyl
Accession: SCV000793104.1
Submitted: (Jul 10, 2018)
Evidence details
Publications
PubMed (2)
Pathogenic
(Feb 18, 2020)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Invitae
Accession: SCV001219595.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change creates a premature translational stop signal (p.Glu295*) in the CLN3 gene. It is expected to result in an absent or disrupted protein … (more)
Pathogenic
(Mar 11, 2021)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV001519540.1
Submitted: (Mar 17, 2021)
Evidence details
Publications
PubMed (6)
Comment:
Variant summary: CLN3 c.883G>T (p.Glu295X) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein … (more)
Pathogenic
(Oct 08, 2020)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV001773508.1
Submitted: (Aug 05, 2021)
Evidence details
Comment:
Identified in a patient with suspected JNCL who did not have a second identifiable CLN3 variant (Kousi et al., 2012); Nonsense variant predicted to result … (more)
Pathogenic
(Aug 10, 2021)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 3
Allele origin: germline
Nilou-Genome Lab
Accession: SCV001977443.1
Submitted: (Oct 12, 2021)
Evidence details
probable-pathogenic
(-)
no assertion criteria provided
Method: not provided
Juvenile neuronal ceroid lipofuscinosis
Allele origin: not provided
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)
Accession: SCV000082109.1
Submitted: (May 19, 2013)
Comment:
FinDis database variant: This variant was not found or characterized by our laboratory, data were collected from public sources: see reference
Evidence details
Comment:
Converted during submission to Likely pathogenic.

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Novel homozygous CLN3 missense variant in isolated retinal dystrophy: A case report and electron microscopic findings. Mizobuchi K Molecular genetics & genomic medicine 2020 PMID: 32441891
Considerations in multi-gene panel testing in pediatric ophthalmology. Turriff AE Journal of AAPOS : the official publication of the American Association for Pediatric Ophthalmology and Strabismus 2019 PMID: 30769084
Detailed Clinical Phenotype and Molecular Genetic Findings in CLN3-Associated Isolated Retinal Degeneration. Ku CA JAMA ophthalmology 2017 PMID: 28542676
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Xiong HY Science (New York, N.Y.) 2015 PMID: 25525159
Update of the mutation spectrum and clinical correlations of over 360 mutations in eight genes that underlie the neuronal ceroid lipofuscinoses. Kousi M Human mutation 2012 PMID: 21990111
Carrier testing for severe childhood recessive diseases by next-generation sequencing. Bell CJ Science translational medicine 2011 PMID: 21228398
Heterogeneity of late-infantile neuronal ceroid lipofuscinosis. Zhong N Genetics in medicine : official journal of the American College of Medical Genetics 2000 PMID: 11339651
Spectrum of mutations in the Batten disease gene, CLN3. Munroe PB American journal of human genetics 1997 PMID: 9311735

Text-mined citations for rs121434286...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 30, 2021