rs397516745

chrX-120469114-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2 PP3_Moderate

The NM_002294.3(LAMP2):c.56T>G(p.Leu19Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 Uncertain significance (★).

• Frequency: Genomes: not found (cov: 23)
• Consequence: LAMP2 NM_002294.3 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 3.45

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]

ACMG classification

Verdict is Uncertain_significance. Variant got 4 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.907

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LAMP2	NM_002294.3	c.56T>G	p.Leu19Arg	missense_variant	1/9	ENST00000200639.9
LAMP2	NM_001122606.1	c.56T>G	p.Leu19Arg	missense_variant	1/9
LAMP2	NM_013995.2	c.56T>G	p.Leu19Arg	missense_variant	1/9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LAMP2	ENST00000200639.9	c.56T>G	p.Leu19Arg	missense_variant	1/9	1	NM_002294.3	P3
LAMP2	ENST00000434600.6	c.56T>G	p.Leu19Arg	missense_variant	1/9	1		A1
LAMP2	ENST00000371335.4	c.56T>G	p.Leu19Arg	missense_variant	1/9	1		A1
LAMP2	ENST00000706600.1	c.56T>G	p.Leu19Arg	missense_variant	1/9

Frequencies

GnomAD3 genomes Cov.: 23

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 23

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

Feb 03, 2011

Variant classified as Uncertain Significance - Favor Pathogenic. The Leu19Arg va riant has not been reported in the literature and has not been previously detect ed in over 2000 Caucasian chromosomes tested at our laboratory. This low freque ncy supports a pathogenic role as does the fact that it was detected in an indiv idual with a clinical presentation and family history consistent with Danon dise ase. However, although leucine (Leu) at position 19 is conserved among many mam malian species as well as more distant species (chicken, frog), one mammalian sp ecies (elephant) carries a different amino acid, reducing the likelihood that th e change is pathogenic. Importantly, pathogenic missense variants are very rare in the LAMP2 gene (most disease causing variants cause a loss of function). In summary, additional evidence is needed to determine the significance of this var iant. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.34
CardioboostCm	Benign	0.081
BayesDel_addAF	Pathogenic	0.17	D
BayesDel_noAF	Uncertain	0.010
Cadd	Uncertain	24
Dann	Uncertain	0.99
FATHMM_MKL	Benign	0.50	D
LIST_S2	Benign	0.80	T;T;T
M_CAP	Benign	0.077	D
MetaRNN	Pathogenic	0.91	D;D;D
MetaSVM	Benign	-0.45	T
MutationAssessor	Uncertain	2.4	M;M;M
MutationTaster	Benign	1.0	D;D;D;D
PrimateAI	Benign	0.44	T
PROVEAN	Benign	-2.2	N;N;N
REVEL	Uncertain	0.32
Sift	Uncertain	0.0080	D;D;D
Sift4G	Benign	0.077	T;T;T
Polyphen		0.91, 0.97	.;P;D
Vest4		0.87
MutPred		0.73		Loss of stability (P = 0.0096);Loss of stability (P = 0.0096);Loss of stability (P = 0.0096);
MVP		0.90
MPC		1.0
ClinPred		0.96	D
GERP RS		4.1
RBP_binding_hub_radar		0.92
RBP_regulation_power_radar		2.0
Varity_R		0.40
gMVP		0.83

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs397516745; hg19: chrX-119602969;