NM_006493.4(CLN5):c.84G>A (p.Trp28Ter) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Aug 23, 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_006493.4(CLN5):c.84G>A (p.Trp28Ter)]

NM_006493.4(CLN5):c.84G>A (p.Trp28Ter)

CLN5:CLN5 intracellular trafficking protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_006493.4(CLN5):c.84G>A (p.Trp28Ter)
  • NC_000013.11:g.76992182G>A
  • NG_009064.1:g.5259G>A
  • NM_001366624.2:c.84G>A
  • NM_006493.4:c.84G>AMANE SELECT
  • NP_001353553.1:p.Trp28Ter
  • NP_006484.2:p.Trp28Ter
  • LRG_692t1:c.231G>A
  • LRG_692:g.5259G>A
  • NC_000013.10:g.77566317G>A
  • NM_006493.2:c.231G>A
Protein change:
dbSNP: rs200348035
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001366624.2:c.84G>A - nonsense - [Sequence Ontology: SO:0001587]
  • NM_006493.4:c.84G>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)
SCV000620322GeneDxcriteria provided, single submitter
Likely pathogenic
(Aug 23, 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, SCV000620322.1

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


A variant that is likely pathogenic has been identified in the CLN5 gene. The W77X nonsense variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The W77X variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The W77X variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.

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

Last Updated: Nov 27, 2021

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