rs730880478
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_002294.3(LAMP2):c.73C>T(p.Arg25Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000391 in 1,100,297 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 13 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R25Q) has been classified as Likely benign.
Frequency
Consequence
NM_002294.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LAMP2 | NM_002294.3 | c.73C>T | p.Arg25Trp | missense_variant | Exon 2 of 9 | ENST00000200639.9 | NP_002285.1 | |
LAMP2 | NM_001122606.1 | c.73C>T | p.Arg25Trp | missense_variant | Exon 2 of 9 | NP_001116078.1 | ||
LAMP2 | NM_013995.2 | c.73C>T | p.Arg25Trp | missense_variant | Exon 2 of 9 | NP_054701.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LAMP2 | ENST00000200639.9 | c.73C>T | p.Arg25Trp | missense_variant | Exon 2 of 9 | 1 | NM_002294.3 | ENSP00000200639.4 | ||
LAMP2 | ENST00000434600.6 | c.73C>T | p.Arg25Trp | missense_variant | Exon 2 of 9 | 1 | ENSP00000408411.2 | |||
LAMP2 | ENST00000371335.4 | c.73C>T | p.Arg25Trp | missense_variant | Exon 2 of 9 | 1 | ENSP00000360386.4 | |||
LAMP2 | ENST00000706600.1 | c.73C>T | p.Arg25Trp | missense_variant | Exon 2 of 9 | ENSP00000516464.1 |
Frequencies
GnomAD3 genomes AF: 0.000126 AC: 14AN: 111330Hom.: 0 Cov.: 23 AF XY: 0.000179 AC XY: 6AN XY: 33546
GnomAD3 exomes AF: 0.0000296 AC: 5AN: 169128Hom.: 0 AF XY: 0.0000536 AC XY: 3AN XY: 55958
GnomAD4 exome AF: 0.0000293 AC: 29AN: 988923Hom.: 0 Cov.: 19 AF XY: 0.0000249 AC XY: 7AN XY: 280819
GnomAD4 genome AF: 0.000126 AC: 14AN: 111374Hom.: 0 Cov.: 23 AF XY: 0.000179 AC XY: 6AN XY: 33602
ClinVar
Submissions by phenotype
not provided Uncertain:3
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Identified in a patient with sudden unexplained death and negative autopsy findings in the published literature (Shanks et al., 2018); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 29915097) -
Danon disease Uncertain:2
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This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 25 of the LAMP2 protein (p.Arg25Trp). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with sudden unexplained death (PMID: 29915097). ClinVar contains an entry for this variant (Variation ID: 180868). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
not specified Uncertain:1
Variant summary: LAMP2 c.73C>T (p.Arg25Trp) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 3e-05 in 169128 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. c.73C>T has been reported in the literature in an individual affected with sudden unexplained death (Shanks_2018). This report does not provide unequivocal conclusions about association of the variant with Danon Disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 29915097). ClinVar contains an entry for this variant (Variation ID: 180868). Based on the evidence outlined above, the variant was classified as uncertain significance. -
Cardiovascular phenotype Uncertain:1
The p.R25W variant (also known as c.73C>T), located in coding exon 2 of the LAMP2 gene, results from a C to T substitution at nucleotide position 73. The arginine at codon 25 is replaced by tryptophan, an amino acid with dissimilar properties. Based on data from gnomAD, the T allele has an overall frequency of 0.003% (6/190735) total alleles studied, with 3 hemizygotes observed. The highest observed frequency was 0.02% (4/18373) of African/African American alleles. This amino acid position is poorly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at