NM_013995.2(LAMP2):c.-26_-15dup AND multiple conditions

Clinical significance:Uncertain significance (Last evaluated: Oct 10, 2014)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000157988.1

Allele description [Variation Report for NM_013995.2(LAMP2):c.-26_-15dup]

NM_013995.2(LAMP2):c.-26_-15dup

Gene:
LAMP2:lysosomal associated membrane protein 2 [Gene - OMIM - HGNC]
Variant type:
Duplication
Cytogenetic location:
Xq24
Genomic location:
Preferred name:
NM_013995.2(LAMP2):c.-26_-15dup
HGVS:
  • NC_000023.11:g.120469188_120469199dup
  • NG_007995.1:g.5155_5166dup
  • NM_001122606.1:c.-26_-15dup
  • NM_002294.2:c.-26_-15dup
  • NM_013995.2:c.-26_-15dup
  • LRG_749t1:c.-26_-15dup
  • LRG_749t2:c.-26_-15dup
  • LRG_749t3:c.-26_-15dup
  • LRG_749:g.5155_5166dup
  • NC_000023.10:g.119603043_119603054dup
  • NM_001122606.1:c.-26_-15dupGCCGTCGCCGCC
Links:
dbSNP: rs1556124241
NCBI 1000 Genomes Browser:
rs1556124241
Molecular consequence:
  • NM_001122606.1:c.-26_-15dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_002294.2:c.-26_-15dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_013995.2:c.-26_-15dup - 5 prime UTR variant - [Sequence Ontology: SO:0001623]

Condition(s)

Name:
Danon disease
Synonyms:
PSEUDOGLYCOGENOSIS II; GSD IIb; LYSOSOMAL GLYCOGEN STORAGE DISEASE WITHOUT ACID MALTASE DEFICIENCY; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0010281; MedGen: C0878677; Orphanet: 34587; OMIM: 300257
Name:
Cardiomyopathy (CMYO)
Identifiers:
MONDO: MONDO:0004994; MedGen: C0878544; Human Phenotype Ontology: HP:0001638

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000207923GeneDxcriteria provided, single submitter
Uncertain significance
(Oct 10, 2014)
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, SCV000207923.2

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

Description

c.-26_-15dupGCCGTCGCCGCC in exon 1 of the LAMP2 gene (NM_001122606.1). The c.-26_-15dupGCCGTCGCCGCC variant in the LAMP2 gene has not been reported as a disease-causing mutation or as a benign polymorphism. Several in silico splice prediction algorithms predict this variant does not affect splicing. This variant is located in the 5' untranslated region (UTR) of the LAMP2 gene and a small deletion in this region has been reported previously both as a benign polymorphism and in association with Danon disease. c.-26_-15dupGCCGTCGCCGCC 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 mutation or a rare benign variant. The variant is found in CARDIOMYOPATHY,HCM panel(s).

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

Last Updated: Oct 7, 2021

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