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NM_001042432.2(CLN3):c.764G>A (p.Arg255Lys) 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:
RCV000482549.1

Allele description [Variation Report for NM_001042432.2(CLN3):c.764G>A (p.Arg255Lys)]

NM_001042432.2(CLN3):c.764G>A (p.Arg255Lys)

Gene:
CLN3:CLN3 lysosomal/endosomal transmembrane protein, battenin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16p12.1
Genomic location:
Preferred name:
NM_001042432.2(CLN3):c.764G>A (p.Arg255Lys)
HGVS:
  • NC_000016.10:g.28484032C>T
  • NG_008654.2:g.13271G>A
  • NM_000086.2:c.764G>A
  • NM_001042432.2:c.764G>AMANE SELECT
  • NM_001286104.2:c.692G>A
  • NM_001286105.2:c.464G>A
  • NM_001286109.2:c.530G>A
  • NM_001286110.2:c.602G>A
  • NP_000077.1:p.Arg255Lys
  • NP_001035897.1:p.Arg255Lys
  • NP_001035897.1:p.Arg255Lys
  • NP_001273033.1:p.Arg231Lys
  • NP_001273034.1:p.Arg155Lys
  • NP_001273038.1:p.Arg177Lys
  • NP_001273039.1:p.Arg201Lys
  • LRG_689t1:c.764G>A
  • LRG_689t2:c.764G>A
  • LRG_689:g.13271G>A
  • LRG_689p1:p.Arg255Lys
  • LRG_689p2:p.Arg255Lys
  • NC_000016.9:g.28495353C>T
  • NM_001042432.1:c.764G>A
Protein change:
R155K
Links:
dbSNP: rs1064795604
NCBI 1000 Genomes Browser:
rs1064795604
Molecular consequence:
  • NM_000086.2:c.764G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042432.2:c.764G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001286104.2:c.692G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001286105.2:c.464G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001286109.2:c.530G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001286110.2:c.602G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: CN517202

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000571579GeneDx
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, SCV000571579.3

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

Description

A variant of uncertain significance has been identified in the CLN3 gene. The R255K variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The R255K variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position that is not conserved and in silico analysis predicts this variant likely does not alter the protein structure/function. However, the R255K variant 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. 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: Apr 23, 2022