NM_001042432.2(CLN3):c.883G>T (p.Glu295Ter) AND not provided

Clinical significance:Pathogenic (Last evaluated: Oct 8, 2020)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV001552759.2

Allele description [Variation Report for NM_001042432.2(CLN3):c.883G>T (p.Glu295Ter)]

NM_001042432.2(CLN3):c.883G>T (p.Glu295Ter)

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.883G>T (p.Glu295Ter)
HGVS:
  • NC_000016.10:g.28482500C>A
  • NG_008654.2:g.14803G>T
  • NM_000086.2:c.883G>T
  • NM_001042432.2:c.883G>TMANE SELECT
  • NM_001286104.2:c.811G>T
  • NM_001286105.2:c.583G>T
  • NM_001286109.2:c.649G>T
  • NM_001286110.2:c.721G>T
  • NP_000077.1:p.Glu295Ter
  • NP_001035897.1:p.Glu295Ter
  • NP_001035897.1:p.Glu295Ter
  • NP_001273033.1:p.Glu271Ter
  • NP_001273034.1:p.Glu195Ter
  • NP_001273038.1:p.Glu217Ter
  • NP_001273039.1:p.Glu241Ter
  • LRG_689t1:c.883G>T
  • LRG_689t2:c.883G>T
  • LRG_689:g.14803G>T
  • LRG_689p1:p.Glu295Ter
  • LRG_689p2:p.Glu295Ter
  • NC_000016.9:g.28493821C>A
  • NM_000086.2:c.883G>T
  • NM_001042432.1:c.883G>T
Protein change:
E195*
Links:
dbSNP: rs121434286
NCBI 1000 Genomes Browser:
rs121434286
Molecular consequence:
  • NM_000086.2:c.883G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001042432.2:c.883G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001286104.2:c.811G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001286105.2:c.583G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001286109.2:c.649G>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001286110.2:c.721G>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV001773508GeneDxcriteria provided, single submitter
Pathogenic
(Oct 8, 2020)
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, SCV001773508.1

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

Description

Identified in a patient with suspected JNCL who did not have a second identifiable CLN3 variant (Kousi et al., 2012); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss-of-function is a known mechanism of disease; Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 21990111, 31741823, 28542676, 31568712, 30769084, 11339651, 25525159, 21228398)

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

Last Updated: Dec 4, 2021

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