GENE REFERENCE / HGNC:4451

GPC3

glypican 3

protein-coding geneXq26.2Gene information

What does this gene do?

The GPC3 gene provides instructions for making a protein called glypican 3. This protein is one of several glypicans in humans, each of which consists of a core protein attached to long sugar molecules called heparan sulfate chains. Glypicans are anchored to the outer cell membrane, where they interact with a variety of other proteins outside the cell. Glypicans appear to play important roles in development before birth. These proteins are involved in numerous cell functions, including regulating cell growth and division (cell proliferation) and cell survival.

Several studies have found that glypican 3 interacts with other proteins at the surface of cells to restrain cell proliferation. Specifically, glypican 3 blocks (inhibits) a developmental pathway called the hedgehog signaling pathway. This pathway is critical for cell proliferation, cell specialization, and the normal shaping (patterning) of many parts of the body during embryonic development.

Researchers believe that in some cell types, glypican 3 may act as a tumor suppressor, which is a protein that prevents cells from growing and dividing in an uncontrolled way to form a cancerous tumor. Glypican 3 may also cause some types of cells to self-destruct (undergo apoptosis) when they are no longer needed, which can help keep growth in check.

Although glypican 3 is known primarily as an inhibitor of cell growth and cell division, in some tissues it appears to have the opposite effect. Research suggests that in certain types of cells, such as cells in the liver, glypican 3 may interact with proteins called growth factors to promote cell growth and cell division.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2017-07.

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
Simpson-Golabi-Behmel syndromeMONDO:0010731 · Evaluated 2019-12-31	X-linked	DefinitiveIntellectual Disability and Autism 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: 1,339
Submissions for variants in or overlapping this gene: 1,887
Submissions explicitly reporting this gene: 1,664
Alleles reported pathogenic / likely pathogenic: 116
VariationIDs with uncertain significance: 503
VariationIDs with conflicting classifications: 47

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 GPC3?

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 116 alleles in GPC3 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 GPC3.

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

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