GENE REFERENCE / HGNC:17893

PGAP2

post-GPI attachment to proteins 2

protein-coding gene11p15.4Gene information

What does this gene do?

The PGAP2 gene provides instructions for making a protein that modifies a molecule called a glycosylphosphosphatidylinositol (GPI) anchor. The GPI anchor attaches (binds) to various proteins and then binds them to the outer surface of the cell membrane, ensuring that they are available when needed. The GPI anchor is made up of many different pieces and is assembled in a cell structure called the endoplasmic reticulum, which is involved in protein processing and transport. The anchor is then transferred to a different cell structure called the Golgi apparatus, which modifies newly produced enzymes and other proteins. In the Golgi apparatus, the PGAP2 protein assists in attaching a molecule called a saturated fatty acid to the anchor. This saturated fatty acid is likely needed to help transport and attach the anchor to the fat-rich cell membrane.

Source: MedlinePlus, National Library of Medicine. Source publication: 2020-08-18. Source review: 2013-07.

ClinGen reviews

We found no matching ClinGen review in the data used here. This does not rule out a link between the gene and a condition.

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: 199
Submissions for variants in or overlapping this gene: 244
Submissions explicitly reporting this gene: 212
Alleles reported pathogenic / likely pathogenic: 18
VariationIDs with uncertain significance: 81
VariationIDs with conflicting classifications: 6

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 PGAP2?

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 18 alleles in PGAP2 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 PGAP2.

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

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