rs876657846
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_013995.2(LAMP2):c.1222C>G(p.Gln408Glu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 10/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 23)
Exomes 𝑓: 9.1e-7 ( 0 hom. 1 hem. )
Failed GnomAD Quality Control
Consequence
LAMP2
NM_013995.2 missense
NM_013995.2 missense
Scores
2
1
10
Clinical Significance
Conservation
PhyloP100: 9.60
Publications
1 publications found
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]
LAMP2 Gene-Disease associations (from GenCC):
- Danon diseaseInheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), Orphanet, ClinGen, Genomics England PanelApp
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_013995.2. You can select a different transcript below to see updated ACMG assignments.
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| LAMP2 | TSL:1 | c.1222C>G | p.Gln408Glu | missense | Exon 9 of 9 | ENSP00000360386.4 | P13473-2 | ||
| LAMP2 | TSL:1 MANE Select | c.1093+2565C>G | intron | N/A | ENSP00000200639.4 | P13473-1 | |||
| LAMP2 | TSL:1 | c.1093+2565C>G | intron | N/A | ENSP00000408411.2 | P13473-3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
23
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 9.12e-7 AC: 1AN: 1097016Hom.: 0 Cov.: 29 AF XY: 0.00000276 AC XY: 1AN XY: 362470 show subpopulations
GnomAD4 exome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1
AN:
1097016
Hom.:
Cov.:
29
AF XY:
AC XY:
1
AN XY:
362470
show subpopulations
African (AFR)
AF:
AC:
0
AN:
26364
American (AMR)
AF:
AC:
0
AN:
35196
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19368
East Asian (EAS)
AF:
AC:
0
AN:
30144
South Asian (SAS)
AF:
AC:
0
AN:
54117
European-Finnish (FIN)
AF:
AC:
0
AN:
40500
Middle Eastern (MID)
AF:
AC:
0
AN:
4127
European-Non Finnish (NFE)
AF:
AC:
1
AN:
841152
Other (OTH)
AF:
AC:
0
AN:
46048
GnomAD4 genome
GnomAD4 genome
Cov.:
23
ClinVar
ClinVar submissions
View on ClinVar Significance:Uncertain significance
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
1
-
not specified (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
DANN
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Benign
T
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D
MetaSVM
Benign
T
PhyloP100
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MVP
ClinPred
D
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
Publications
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