NM_017882.3(CLN6):c.167G>A (p.Trp56Ter) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Mar 22, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_017882.3(CLN6):c.167G>A (p.Trp56Ter)]

NM_017882.3(CLN6):c.167G>A (p.Trp56Ter)

CLN6:CLN6 transmembrane ER protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_017882.3(CLN6):c.167G>A (p.Trp56Ter)
  • NC_000015.10:g.68218567C>T
  • NG_008764.2:g.43645G>A
  • NM_017882.3:c.167G>AMANE SELECT
  • NP_060352.1:p.Trp56Ter
  • LRG_832t1:c.167G>A
  • LRG_832:g.43645G>A
  • LRG_832p1:p.Trp56Ter
  • NC_000015.9:g.68510905C>T
  • NM_017882.2:c.167G>A
Protein change:
dbSNP: rs1057520571
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_017882.3:c.167G>A - nonsense - [Sequence Ontology: SO:0001587]


MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000516071GeneDxcriteria provided, single submitter
Likely pathogenic
(Mar 22, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000516071.4

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


The W56X variant in the CLN6 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The W56X variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The W56X variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded.

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

Last Updated: Feb 27, 2021

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