PYGO2
protein-codingpygopus family PHD finger 2, the group of Wnt enhanceosome complex|PHD finger proteins
Gene summary
Predicted to enable chromatin binding activity; histone acetyltransferase regulator activity; and histone binding activity. Predicted to be involved in Wnt signaling pathway. Predicted to act upstream of or within several processes, including canonical Wnt signaling pathway; lens development in camera-type eye; and spermatid nucleus differentiation. Located in nucleoplasm. Part of beta-catenin-TCF complex. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to PYGO2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_138300.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 72 | 72 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 75 | 0 | 0 | 75 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_612157.1 | 3 | MANE Select | |
| Ensembl | ENSP00000357442.2 | 3 | MANE Select | |
| Ensembl | ENSP00000357441.1 | 2 | Standard | |
| Ensembl | ENSP00000357441.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Signaling by WNT
- Signal Transduction
- Wnt Canonical
- Formation of the beta-catenin:TCF transactivating complex
- TCF dependent signaling in response to WNT
Biological Process
- in utero embryonic development
- kidney development
- lens development in camera-type eye
- spermatid nucleus differentiation
- brain development
Molecular Function
- chromatin binding
- protein binding
- histone acetyltransferase regulator activity
- histone binding
- metal ion binding
Cellular Component
- nucleoplasm
- beta-catenin-TCF complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000368457
- Coding exons
- 3
- Length
- 6828
- Individuals with no LoFs
- 125657
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 125659
- p
- 0.00000796
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.10 | 161 | 205 | 0.784 | 0.0000109 | 2584 |
| Missense (PolyPhen) | 39 | 62.139 | 0.62762 | 707 | ||
| Synonymous | -0.865 | 91 | 81.1 | 1.12 | 0.00000457 | 886 |
| Loss of Function | 3.01 | 0 | 10.6 | 0.00 | 6.41e-7 | 116 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in signal transduction through the Wnt pathway.;
Recessive Scores
- pRec
- 0.116
Intolerance Scores
- LoFtool
- 0.176
- RVIS EVS
- -0.34
- RVIS percentile EVS
- 30.37
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.949
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |