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NM_002294.3(LAMP2):c.277G>A (p.Gly93Arg) AND not specified

Germline classification:
Likely benign (1 submission)
Last evaluated:
Mar 4, 2014
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:
RCV000156356.4

Allele description [Variation Report for NM_002294.3(LAMP2):c.277G>A (p.Gly93Arg)]

NM_002294.3(LAMP2):c.277G>A (p.Gly93Arg)

Gene:
LAMP2:lysosomal associated membrane protein 2 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq24
Genomic location:
Preferred name:
NM_002294.3(LAMP2):c.277G>A (p.Gly93Arg)
HGVS:
  • NC_000023.11:g.120455477C>T
  • NG_007995.1:g.18873G>A
  • NM_001122606.1:c.277G>A
  • NM_002294.3:c.277G>AMANE SELECT
  • NM_013995.2:c.277G>A
  • NP_001116078.1:p.Gly93Arg
  • NP_002285.1:p.Gly93Arg
  • NP_002285.1:p.Gly93Arg
  • NP_054701.1:p.Gly93Arg
  • LRG_749t1:c.277G>A
  • LRG_749t2:c.277G>A
  • LRG_749t3:c.277G>A
  • LRG_749:g.18873G>A
  • LRG_749p1:p.Gly93Arg
  • LRG_749p2:p.Gly93Arg
  • LRG_749p3:p.Gly93Arg
  • NC_000023.10:g.119589332C>T
  • NM_002294.2:c.277G>A
Protein change:
G93R
Links:
dbSNP: rs727504953
NCBI 1000 Genomes Browser:
rs727504953
Molecular consequence:
  • NM_001122606.1:c.277G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002294.3:c.277G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_013995.2:c.277G>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
AllHighlyPenetrant
Identifiers:
MedGen: CN169374

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000206074Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
criteria provided, single submitter

(LMM Criteria)		Likely benign
(Mar 4, 2014) 		germlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot provided11not providednot providednot providedclinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]
PMID:
24033266
PMCID:
PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000206074.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)

Description

Gly93Arg in exon 3 of LAMP2: This variant is not expected to have clinical signi ficance due to a lack of conservation across species, including mammals. Of note , marmoset, squirrel monkey, tree shrew, guinea pig, and rat have an arginine (A rg) at this position. Furthermore, nearly all disease-causing variants in LAMP2 have been truncating loss of function variants, while this is a missense variant . Gly93Arg in exon 3 of LAMP2 (allele frequency = n/a)

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot provided1not provided1not provided

Last Updated: Feb 28, 2024