NM_017882.3(CLN6):c.316C>T (p.Arg106Cys) AND not provided

Clinical significance:Uncertain significance (Last evaluated: Nov 5, 2014)

Review status:2 stars out of maximum of 4 stars

criteria provided, multiple submitters, no conflicts

Based on:
2 submissions [Details]
Record status:

Allele description [Variation Report for NM_017882.3(CLN6):c.316C>T (p.Arg106Cys)]

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

CLN6:CLN6 transmembrane ER protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_017882.3(CLN6):c.316C>T (p.Arg106Cys)
Other names:
  • NC_000015.10:g.68211845G>A
  • NG_008764.2:g.50367C>T
  • NM_017882.3:c.316C>TMANE SELECT
  • NP_060352.1:p.Arg106Cys
  • LRG_832t1:c.316C>T
  • LRG_832:g.50367C>T
  • LRG_832p1:p.Arg106Cys
  • NC_000015.9:g.68504183G>A
  • NM_017882.2:c.316C>T
Protein change:
dbSNP: rs202226970
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_017882.3:c.316C>T - missense variant - [Sequence Ontology: SO:0001583]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000230372EGL Genetic Diagnostics, Eurofins Clinical Diagnosticscriteria provided, single submitter
Uncertain significance
(Nov 5, 2014)
germlineclinical testing

Citation Link,

SCV000240669GeneDxcriteria provided, single submitter
Uncertain significance
(Sep 30, 2013)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Details of each submission

From EGL Genetic Diagnostics, Eurofins Clinical Diagnostics, SCV000230372.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000240669.11

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided


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 a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This variant is a non-conservative amino acid substitution of a positively charged Arginine residue with an uncharged Cysteine residue, and the addition of a Cysteine may alter disulfide bonds and the secondary structure of the protein. However, the variant alters a position in the protein that is not conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether Arg106Cys is a disease-causing mutation or a rare benign variant. The variant is found in EPILEPSY panel(s).

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 8, 2021

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