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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002635911	Ambry Genetics	criteria provided, single submitter (Ambry Variant Classification Scheme 2023)	Likely benign (Feb 14, 2022)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 24503780, 27532257 Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002635911

Ambry Genetics

criteria provided, single submitter

(Ambry Variant Classification Scheme 2023)

Likely benign
(Feb 14, 2022)

germline

clinical testing

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

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical 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.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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