GENE REFERENCE / HGNC:1665

SCARB2

scavenger receptor class B member 2

protein-coding gene4q21.1Gene information

What does this gene do?

The SCARB2 gene provides instructions for making a protein called lysosomal integral membrane protein-2 (LIMP-2). As its name suggests, this protein is primarily found in the membrane of cellular structures called lysosomes, which are specialized compartments that digest and recycle materials. Before moving to the lysosome, the LIMP-2 protein is processed in a cellular structure called the endoplasmic reticulum. There, LIMP-2 attaches to an enzyme called beta-glucocerebrosidase and transports it to the lysosome. In lysosomes, beta-glucocerebrosidase breaks down a fatty substance called glucocerebroside. The LIMP-2 protein remains in the lysosomal membrane after transporting beta-glucocerebrosidase and is important for the stability of these structures.

The LIMP-2 protein has additional functions outside the lysosome. In the heart, the protein is found in regions known as intercalated discs, which connect individual heart muscle cells together to form strong fibers. The LIMP-2 protein appears to play a role when the heart muscle is abnormally enlarged and has to work harder than normal, although its exact function is not clear.

The LIMP-2 protein is sometimes found in the outer membrane that surrounds the cell. Certain viruses can attach to LIMP-2, which allows them to enter and infect the cell. In particular, enterovirus 71 and certain strains of coxsackievirus (A7, A14, and A16), which cause a viral infection known as hand, foot, and mouth disease, use the LIMP-2 protein.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2016-06.

ClinGen reviews

ClinGen reviews the evidence linking a particular gene to a condition. Each rating below describes the strength of that link. It does not classify a variant in your DNA file.

Condition	Inheritance	Evidence
progressive myoclonus epilepsyMONDO:0020074 · Evaluated 2020-08-23	Autosomal recessive	DefinitiveEpilepsy Gene Curation Expert Panel

ClinVar records

These numbers show what has been submitted to ClinVar. They cannot tell you how likely you are to have a condition.

Submitted alleles: 595
Submissions for variants in or overlapping this gene: 1,024
Submissions explicitly reporting this gene: 988
Alleles reported pathogenic / likely pathogenic: 40
VariationIDs with uncertain significance: 235
VariationIDs with conflicting classifications: 20

The rows count different things: alleles, submissions or VariationIDs. Their categories can overlap, so do not add them together. Pathogenic/likely pathogenic counts exclude structural variants that merely overlap a gene. A dash in the source means “not reported,” not zero.

NCBI produces the gene-summary file each week using counts recorded at the start of the month. The numbers may differ from those on the live ClinVar website. Read the field definitions ↗

View this gene in ClinVar ↗

YOUR DNA FILE

Can your DNA file tell you about SCARB2?

From a DNA test kit (such as 23andMe, AncestryDNA or MyHeritage). These kits check a fixed list of about 600,000 to 700,000 positions across your whole genome. ClinVar lists 40 alleles in SCARB2 reported as pathogenic or likely pathogenic. A kit checks only some of these positions, and often none of them.

From whole genome sequencing (a VCF file). Sequencing reads most of your genome. Your file lists the places where your DNA differs from the reference genome. Some regions are hard to sequence, including parts of some genes that have near-identical copies elsewhere, and a VCF file does not record which positions were read well.

If a variant is not in your file, that does not mean you don’t have it.

What BioDecode checks

BioDecode compares every variant in your file with ClinVar, on your own computer. For each match, it shows the ClinVar classification, the review status and the condition it was reported for. Your file is not uploaded.

A ClinVar classification applies to one particular variant and the condition it was reported for. It does not tell you about other variants in SCARB2.

BioDecode cannot fill gaps in your test, diagnose a condition or replace clinical testing.

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