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NM_002294.3(LAMP2):c.472A>G (p.Thr158Ala) AND Cardiovascular phenotype

Germline classification:
Likely benign (1 submission)
Last evaluated:
Feb 14, 2022
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:
RCV002336129.2

Allele description [Variation Report for NM_002294.3(LAMP2):c.472A>G (p.Thr158Ala)]

NM_002294.3(LAMP2):c.472A>G (p.Thr158Ala)

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.472A>G (p.Thr158Ala)
HGVS:
  • NC_000023.11:g.120449054T>C
  • NG_007995.1:g.25296A>G
  • NM_001122606.1:c.472A>G
  • NM_002294.3:c.472A>GMANE SELECT
  • NM_013995.2:c.472A>G
  • NP_001116078.1:p.Thr158Ala
  • NP_002285.1:p.Thr158Ala
  • NP_002285.1:p.Thr158Ala
  • NP_054701.1:p.Thr158Ala
  • LRG_749t1:c.472A>G
  • LRG_749t2:c.472A>G
  • LRG_749t3:c.472A>G
  • LRG_749:g.25296A>G
  • LRG_749p1:p.Thr158Ala
  • LRG_749p2:p.Thr158Ala
  • LRG_749p3:p.Thr158Ala
  • NC_000023.10:g.119582909T>C
  • NM_002294.2:c.472A>G
  • c.472A>G
Protein change:
T158A
Links:
dbSNP: rs138374063
NCBI 1000 Genomes Browser:
rs138374063
Molecular consequence:
  • NM_001122606.1:c.472A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_002294.3:c.472A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_013995.2:c.472A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Cardiovascular phenotype
Identifiers:
MedGen: CN230736

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002635911Ambry Genetics
criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)		Likely benign
(Feb 14, 2022) 		germlineclinical testing

PubMed (2)
[See all records that cite these PMIDs]

Citation Link

Help

Summary from all submissions

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

Citations

PubMed

The landscape of genetic variation in dilated cardiomyopathy as surveyed by clinical DNA sequencing.

Pugh TJ, Kelly MA, Gowrisankar S, Hynes E, Seidman MA, Baxter SM, Bowser M, Harrison B, Aaron D, Mahanta LM, Lakdawala NK, McDermott G, White ET, Rehm HL, Lebo M, Funke BH.

Genet Med. 2014 Aug;16(8):601-8. doi: 10.1038/gim.2013.204. Epub 2014 Feb 6.

PubMed [citation]
PMID:
24503780

Reassessment of Mendelian gene pathogenicity using 7,855 cardiomyopathy cases and 60,706 reference samples.

Walsh R, Thomson KL, Ware JS, Funke BH, Woodley J, McGuire KJ, Mazzarotto F, Blair E, Seller A, Taylor JC, Minikel EV, Exome Aggregation Consortium, MacArthur DG, Farrall M, Cook SA, Watkins H.

Genet Med. 2017 Feb;19(2):192-203. doi: 10.1038/gim.2016.90. Epub 2016 Aug 17.

PubMed [citation]
PMID:
27532257
PMCID:
PMC5116235

Details of each submission

From Ambry Genetics, SCV002635911.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (2)

Description

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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

Last Updated: Sep 29, 2024