rs1556114013

chrX-120456677-GT-AA

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP6_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
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• 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]

ACMG classification

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

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 22

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Danon disease Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Invitae

Sep 13, 2023

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1556114013; hg19: chrX-119590532;