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NM_017882.3(CLN6):c.116G>A (p.Arg39His)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely benign(1);Uncertain significance(1)

Review status:
criteria provided, conflicting interpretations
Submissions:
2 (Most recent: Mar 26, 2018)
Last evaluated:
Sep 22, 2016
Accession:
VCV000205153.1
Variation ID:
205153
Description:
single nucleotide variant
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NM_017882.3(CLN6):c.116G>A (p.Arg39His)

Allele ID
202889
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q23
Genomic location
15: 68218618 (GRCh38) GRCh38 UCSC
15: 68510956 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.68218618C>T
NC_000015.9:g.68510956C>T
NG_008764.2:g.43594G>A
... more HGVS
Protein change
R39H
Other names
p.R39H:CGC>CAC
Canonical SPDI
NC_000015.10:68218617:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00003
Exome Aggregation Consortium (ExAC) 0.00001
Links
ClinGen: CA313941
dbSNP: rs779456928
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely benign 1 criteria provided, single submitter Aug 13, 2013 RCV000187080.1
Uncertain significance 1 criteria provided, single submitter Sep 22, 2016 RCV000456247.1
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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
443 458

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Sep 22, 2016)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Invitae
Accession: SCV000549215.2
Submitted: (Mar 14, 2017)
Evidence details
Comment:
This sequence change replaces arginine with histidine at codon 39 of the CLN6 protein (p.Arg39His). The arginine residue is weakly conserved and there is a … (more)
Likely benign
(Aug 13, 2013)
criteria provided, single submitter
Method: clinical testing
not specified
Allele origin: germline
GeneDx
Accession: SCV000240655.11
Submitted: (Mar 26, 2018)
Evidence details
Comment:
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at … (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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There are no citations in ClinVar for this variation. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for rs779456928...

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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 08, 2021