rs876657696
Positions:
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_002294.3(LAMP2):c.294G>A(p.Trp98*) variant causes a stop gained change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Genomes: not found (cov: 20)
Consequence
LAMP2
NM_002294.3 stop_gained
NM_002294.3 stop_gained
Scores
2
2
1
Clinical Significance
Conservation
PhyloP100: 5.24
Genes affected
LAMP2 (HGNC:6501): (lysosomal associated membrane protein 2) The protein encoded by this gene is a member of a family of membrane glycoproteins. This glycoprotein provides selectins with carbohydrate ligands. It may play a role in tumor cell metastasis. It may also function in the protection, maintenance, and adhesion of the lysosome. Alternative splicing of this gene results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 18 ACMG points.
PVS1
Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant X-120455460-C-T is Pathogenic according to our data. Variant chrX-120455460-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 228356.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-120455460-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMP2 | NM_002294.3 | c.294G>A | p.Trp98* | stop_gained | 3/9 | ENST00000200639.9 | NP_002285.1 | |
LAMP2 | NM_001122606.1 | c.294G>A | p.Trp98* | stop_gained | 3/9 | NP_001116078.1 | ||
LAMP2 | NM_013995.2 | c.294G>A | p.Trp98* | stop_gained | 3/9 | NP_054701.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMP2 | ENST00000200639.9 | c.294G>A | p.Trp98* | stop_gained | 3/9 | 1 | NM_002294.3 | ENSP00000200639.4 | ||
LAMP2 | ENST00000434600.6 | c.294G>A | p.Trp98* | stop_gained | 3/9 | 1 | ENSP00000408411.2 | |||
LAMP2 | ENST00000371335.4 | c.294G>A | p.Trp98* | stop_gained | 3/9 | 1 | ENSP00000360386.4 | |||
LAMP2 | ENST00000706600.1 | c.294G>A | p.Trp98* | stop_gained | 3/9 | ENSP00000516464.1 |
Frequencies
GnomAD3 genomes Cov.: 20
GnomAD3 genomes
Cov.:
20
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome Cov.: 20
GnomAD4 genome
Cov.:
20
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Danon disease Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Mar 18, 2015 | The p.Trp98X variant in LAMP2 was absent from large population studies but has b een reported in 2 individuals with Danon disease and segregated with disease in 5 affected relatives from 1 family (Fanin 2006, Spinazzi 2008, Miani 2012). A di fferent DNA change resulting in the same protein change (c.293G>A, p.Trp98X) has also been identified by our laboratory in 1 individual with Danon disease. This nonsense variant leads to a premature termination codon at position 98 and has been shown to reduced LAMP2 mRNA levels, resulting in absent LAMP2 protein in a male patient (Fanin 2006). Loss of function of the LAMP2 gene is an established disease mechanism in individuals with Danon disease. In summary, this variant me ets our criteria to be classified as pathogenic for Danon disease in X-linked do minant manner (http://www.partners.org/personalizedmedicine/LMM) based upon its functional impact and segregation in affected individuals. - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Blueprint Genetics | Jan 17, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
FATHMM_MKL
Uncertain
D
Vest4
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at