PYGO1
protein-codingpygopus family PHD finger 1, the group of PHD finger proteins|Wnt enhanceosome complex
Gene summary
Enables histone H3K4me3 reader activity. Predicted to be involved in kidney development and spermatid nucleus differentiation. Predicted to act upstream of or within several processes, including hematopoietic progenitor cell differentiation; positive regulation of transcription by RNA polymerase II; and spermatid development. Predicted to be located in nucleoplasm. [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 ~50.1 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 PYGO1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001367806.1. 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 | 49 | 49 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 51 | 0 | 0 | 51 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001354735.1 | 3 | MANE Select | |
| Ensembl | ENSP00000457777.1 | 3 | MANE Select | |
| RefSeq | NP_001317255.1 | 3 | Standard | |
| RefSeq | NP_056432.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Wnt-beta-catenin Signaling Pathway in Leukemia
- Signaling by WNT
- Signal Transduction
- Wnt Canonical
- Formation of the beta-catenin:TCF transactivating complex
Biological Process
- kidney development
- hematopoietic progenitor cell differentiation
- spermatid nucleus differentiation
- post-embryonic development
- protein localization to nucleus
Molecular Function
- protein binding
- methylated histone binding
- metal ion binding
Cellular Component
- nucleoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000302000
- Coding exons
- 3
- Length
- 50058
- Individuals with no LoFs
- 125722
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 2
- Defined
- 125724
- p
- 0.00000795
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.109 | 232 | 227 | 1.02 | 0.0000118 | 2773 |
| Missense (PolyPhen) | 73 | 77.159 | 0.9461 | 906 | ||
| Synonymous | -0.542 | 90 | 83.7 | 1.08 | 0.00000462 | 829 |
| Loss of Function | 3.35 | 0 | 13.1 | 0.00 | 8.02e-7 | 151 |
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 | 0.000055 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0000088 | 0.0000088 | rare |
| 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
- 0.117
Intolerance Scores
- RVIS EVS
- 0.2
- RVIS percentile EVS
- 67.19
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.440
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |