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NM_017882.3(CLN6):c.316C>T (p.Arg106Cys)

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Interpretation:
Uncertain significance​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
4 (Most recent: Feb 20, 2020)
Last evaluated:
Dec 14, 2019
Accession:
VCV000197315.5
Variation ID:
197315
Description:
single nucleotide variant
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NM_017882.3(CLN6):c.316C>T (p.Arg106Cys)

Allele ID
194476
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
15q23
Genomic location
15: 68211845 (GRCh38) GRCh38 UCSC
15: 68504183 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000015.10:g.68211845G>A
NC_000015.9:g.68504183G>A
NG_008764.2:g.50367C>T
... more HGVS
Protein change
R106C
Other names
p.R106C:CGC>TGC
Canonical SPDI
NC_000015.10:68211844:G:A
Functional consequence
-
Global minor allele frequency (GMAF)
0.00020 (A)

Allele frequency
Trans-Omics for Precision Medicine (TOPMed) 0.00006
The Genome Aggregation Database (gnomAD) 0.00003
Exome Aggregation Consortium (ExAC) 0.00005
The Genome Aggregation Database (gnomAD), exomes 0.00007
1000 Genomes Project 0.00020
Links
ClinGen: CA245380
dbSNP: rs202226970
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Dec 14, 2019 RCV000458041.5
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Nov 5, 2014 RCV000724319.2
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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
443 458

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Nov 05, 2014)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics
Accession: SCV000230372.5
Submitted: (Sep 19, 2018)
Evidence details
Other databases
http://www.egl-eurofins.com/emvc…
Uncertain significance
(Sep 30, 2013)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000240669.11
Submitted: (Jan 29, 2019)
Evidence details
Comment:
p.Arg106Cys (CGC>TGC): c.316 C>T in exon 4 of the CLN6 gene (NM_017882.2). The Arg106Cys missense change in the CLN6 gene has not been published as … (more)
Uncertain significance
(Dec 14, 2019)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Invitae
Accession: SCV000549212.5
Submitted: (Feb 06, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces arginine with cysteine at codon 106 of the CLN6 protein (p.Arg106Cys). The arginine residue is highly conserved and there is a … (more)
Uncertain significance
(Jan 13, 2018)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001274725.1
Submitted: (Feb 20, 2020)
Evidence details
Comment:
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated … (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
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
http://www.egl-eurofins.com/emvclass/emvclass.php?approved_symbol=CLN6 - - - -

Text-mined citations for rs202226970...

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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