NM_002294.3(LAMP2):c.472A>G (p.Thr158Ala) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 6, 2012
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:: RCV000037419.5

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]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000061076	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Uncertain significance (Jul 6, 2012)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000061076

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Uncertain significance
(Jul 6, 2012)

germline

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	1	1	not provided	not provided	not provided	clinical 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, SCV000061076.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

Description

Variant classified as Uncertain Significance - Favor Benign. The Thr158Ala varia nt in LAMP2 has been identified in 2/6727 European American chromosomes from a b road population by the NHLBI Exome Sequencing Project (http://evs.gs.washington. edu/EVS; dbSNP rs138374063). Threonine (Thr) at position 158 is not conserved in mammals or evolutionarily distant species and elephant carries an alanine (Ala; this variant), suggesting that this change may be tolerated. In addition, compu tational analyses (biochemical amino acid properties, AlignGVGD, PolyPhen2, and SIFT) suggest that this variant may not impact the protein, though this informat ion is not predictive enough to rule out pathogenicity. In summary, the frequenc y of this variant and lack of amino acid conservation suggests that it may be mo re likely benign, but additional information is needed to fully assess its clini cal significance.

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

Last Updated: Sep 29, 2024

ClinVar

Relating variation to medicine