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NM_017882.3(CLN6):c.199-2A>G

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, single submitter
Submissions:
1 (Most recent: Jan 7, 2021)
Last evaluated:
Mar 4, 2019
Accession:
VCV000841102.2
Variation ID:
841102
Description:
single nucleotide variant
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NM_017882.3(CLN6):c.199-2A>G

Allele ID
852067
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q23
Genomic location
15: 68214390 (GRCh38) GRCh38 UCSC
15: 68506728 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
LRG_832:g.47822A>G
LRG_832t1:c.199-2A>G
NC_000015.10:g.68214390T>C
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000015.10:68214389:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00001
Trans-Omics for Precision Medicine (TOPMed) 0.00001
Links
dbSNP: rs1471253353
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Mar 4, 2019 RCV001043252.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CLN6 - - GRCh38
GRCh37
447 462

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Mar 04, 2019)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Invitae
Accession: SCV001206976.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change affects an acceptor splice site in intron 2 of the CLN6 gene. It is expected to disrupt RNA splicing and likely results … (more)

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
Variant late infantile ceroid lipofuscinoses associated with novel mutations in CLN6. Cannelli N Biochemical and biophysical research communications 2009 PMID: 19135028
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547

Text-mined citations for rs1471253353...

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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 Nov 27, 2021