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NM_006493.4(CLN5):c.869G>T (p.Arg290Ile) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Sep 13, 2016
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000483654.1

Allele description [Variation Report for NM_006493.4(CLN5):c.869G>T (p.Arg290Ile)]

NM_006493.4(CLN5):c.869G>T (p.Arg290Ile)

Gene:
CLN5:CLN5 intracellular trafficking protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
13q22.3
Genomic location:
Preferred name:
NM_006493.4(CLN5):c.869G>T (p.Arg290Ile)
HGVS:
  • NC_000013.11:g.77000761G>T
  • NG_009064.1:g.13838G>T
  • NM_001366624.2:c.*318G>T
  • NM_006493.4:c.869G>TMANE SELECT
  • NP_006484.2:p.Arg290Ile
  • LRG_692t1:c.1016G>T
  • LRG_692:g.13838G>T
  • NC_000013.10:g.77574896G>T
  • NM_006493.2:c.1016G>T
Protein change:
R290I
Links:
dbSNP: rs770688728
NCBI 1000 Genomes Browser:
rs770688728
Molecular consequence:
  • NM_001366624.2:c.*318G>T - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
  • NM_006493.4:c.869G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000571671GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Sep 13, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

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

Details of each submission

From GeneDx, SCV000571671.4

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

Description

A variant of uncertain significance has been identified in the CLN5 gene. The R339I variant has not been published as a pathogenic variant, nor has it been reported as a benign variant 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. The R339I variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. However, this substitution occurs at a position that is not conserved. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: Sep 29, 2024