rs1556114013
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP6_Moderate
The NM_002294.3(LAMP2):c.156_157delinsTT(p.Arg53Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. V52V) has been classified as Likely benign.
Frequency
Genomes: not found (cov: 22)
Consequence
LAMP2
NM_002294.3 missense
NM_002294.3 missense
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.43
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 Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP6
Variant X-120456677-GT-AA is Benign according to our data. Variant chrX-120456677-GT-AA is described in ClinVar as [Likely_benign]. Clinvar id is 532014.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LAMP2 | NM_002294.3 | c.156_157delinsTT | p.Arg53Cys | missense_variant | 2/9 | ENST00000200639.9 | |
LAMP2 | NM_001122606.1 | c.156_157delinsTT | p.Arg53Cys | missense_variant | 2/9 | ||
LAMP2 | NM_013995.2 | c.156_157delinsTT | p.Arg53Cys | missense_variant | 2/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LAMP2 | ENST00000200639.9 | c.156_157delinsTT | p.Arg53Cys | missense_variant | 2/9 | 1 | NM_002294.3 | P3 | |
LAMP2 | ENST00000371335.4 | c.156_157delinsTT | p.Arg53Cys | missense_variant | 2/9 | 1 | A1 | ||
LAMP2 | ENST00000434600.6 | c.156_157delinsTT | p.Arg53Cys | missense_variant | 2/9 | 1 | A1 | ||
LAMP2 | ENST00000706600.1 | c.156_157delinsTT | p.Arg53Cys | missense_variant | 2/9 |
Frequencies
GnomAD3 genomes Cov.: 22
GnomAD3 genomes
Cov.:
22
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome Cov.: 22
GnomAD4 genome
Cov.:
22
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Danon disease Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 13, 2023 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at