NM_002294.3(LAMP2):c.139C>T (p.Gln47Ter) AND Danon disease

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 2, 2020
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:: RCV001871756.4

Allele description [Variation Report for NM_002294.3(LAMP2):c.139C>T (p.Gln47Ter)]

NM_002294.3(LAMP2):c.139C>T (p.Gln47Ter)

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.139C>T (p.Gln47Ter)

HGVS:

NC_000023.11:g.120456695G>A
NG_007995.1:g.17655C>T
NM_001122606.1:c.139C>T
NM_002294.3:c.139C>TMANE SELECT
NM_013995.2:c.139C>T
NP_001116078.1:p.Gln47Ter
NP_002285.1:p.Gln47Ter
NP_054701.1:p.Gln47Ter
LRG_749t1:c.139C>T
LRG_749t2:c.139C>T
LRG_749t3:c.139C>T
LRG_749:g.17655C>T
LRG_749p2:p.Gln47Ter
LRG_749p3:p.Gln47Ter
NC_000023.10:g.119590550G>A
NM_002294.2:c.139C>T

Protein change:

Q47*

Links:

dbSNP: rs2147287624

NCBI 1000 Genomes Browser:

rs2147287624

Molecular consequence:

NM_001122606.1:c.139C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_002294.3:c.139C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_013995.2:c.139C>T - nonsense - [Sequence Ontology: SO:0001587]

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

Recent activity

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Caenorhabditis elegans choline-phosphate cytidylyltransferase (Y18H1A.11), partial mRNA
gi|1831505135|ref|NM_001306250.3|

Nucleotide
PREDICTED: Mus musculus spleen tyrosine kinase (Syk), transcript variant X3, mRN...
PREDICTED: Mus musculus spleen tyrosine kinase (Syk), transcript variant X3, mRNA
gi|1907093286|ref|XM_006516897.5|

Nucleotide
Pseudomonas syringae strain PA-4-8B, whole genome shotgun sequencing project
Pseudomonas syringae strain PA-4-8B, whole genome shotgun sequencing project
gi|2183301013|gb|WKCC00000000.1|WKC 0000

Nucleotide
Pseudomonas poae strain PA-2-1F, whole genome shotgun sequencing project
Pseudomonas poae strain PA-2-1F, whole genome shotgun sequencing project
gi|2183302572|gb|WJZX00000000.1|WJZ 0000

Nucleotide
Pseudomonas proteolytica strain PA-6-9F, whole genome shotgun sequencing project
Pseudomonas proteolytica strain PA-6-9F, whole genome shotgun sequencing project
gi|2183300653|gb|WKEW00000000.1|WKE 0000

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002164039	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 2, 2020)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 21415759, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002164039

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 2, 2020)

germline

clinical testing

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

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

Natural history of Danon disease.

Boucek D, Jirikowic J, Taylor M.

Genet Med. 2011 Jun;13(6):563-8. doi: 10.1097/GIM.0b013e31820ad795.

PubMed [citation]

PMID:: 21415759

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002164039.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals with LAMP2-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.Gln47*) in the LAMP2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LAMP2 are known to be pathogenic (PMID: 21415759).

#	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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