GENE REFERENCE / HGNC:9312

PPP2R5D

protein phosphatase 2 regulatory subunit B'delta

protein-coding gene6p21.1Gene information

What does this gene do?

The PPP2R5D gene provides instructions for making a protein called B56-delta (B56δ). This protein is one piece (the B subunit) of an enzyme called protein phosphatase 2A (PP2A). (B56δ is one of several possible B subunits.) The PP2A enzyme removes phosphate groups, consisting of clusters of oxygen and phosphorus atoms, from certain proteins. This process, called dephosphorylation, helps control whether the protein is turned on or off. The B subunit determines which proteins are dephosphorylated by PP2A and regulates the activity of the enzyme.

PP2A removes phosphate groups from proteins that are part of signaling pathways involved in cell growth and turning genes on and off. PP2A enzymes containing the B56δ protein are found mainly in the brain, where they are thought to be primarily involved in controlling the activity of signaling pathways that play roles in the normal development and function of nerve cells (neurons).

Source: MedlinePlus, National Library of Medicine. Source publication: 2021-02-01. Source review: 2017-08.

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
complex neurodevelopmental disorderMONDO:0100038 · Evaluated 2025-04-16	Autosomal dominant	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: 707
Submissions for variants in or overlapping this gene: 1,011
Submissions explicitly reporting this gene: 982
Alleles reported pathogenic / likely pathogenic: 28
VariationIDs with uncertain significance: 308
VariationIDs with conflicting classifications: 29

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 PPP2R5D?

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 28 alleles in PPP2R5D 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 PPP2R5D.

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

Buy BioDecode See a sample report →Check file compatibility →