STPG4
protein-codingsperm-tail PG-rich repeat containing 4
Gene summary
Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in epigenetic programing of male pronucleus. Predicted to act upstream of or within pyrimidine-containing compound catabolic process. Predicted to be located in cytoplasm and nucleus. Predicted to be active in female pronucleus; germinal vesicle; and male pronucleus. [provided by Alliance of Genome Resources, Jul 2025]
- C2orf61
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~109.8 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 STPG4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001163561.2. 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 | 1 | 1 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 1 | 0 | 0 | 1 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001157033.1 | 7 | MANE Select | |
| Ensembl | ENSP00000408527.2 | 7 | MANE Select | |
| RefSeq | NP_775920.1 | 5 | Standard | |
| Ensembl | ENSP00000294947.2 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- chromatin organization
- DNA demethylation of male pronucleus
- C-5 methylation of cytosine
- positive regulation of DNA demethylation
Molecular Function
- chromatin binding
- histone binding
Cellular Component
- female pronucleus
- male pronucleus
- nucleus
- cytoplasm
- germinal vesicle
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000445927
- Coding exons
- 7
- Length
- 109841
- Individuals with no LoFs
- 125720
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 27
- Defined
- 125747
- p
- 0.000107
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.861 | 162 | 134 | 1.21 | 0.00000686 | 1600 |
| Missense (PolyPhen) | 61 | 53.366 | 1.143 | 619 | ||
| Synonymous | -1.39 | 61 | 48.6 | 1.25 | 0.00000266 | 485 |
| Loss of Function | 1.21 | 8 | 12.6 | 0.633 | 5.97e-7 | 163 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00018 | 0.00018 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Maternal factor that plays a role in epigenetic chromatin reprogramming during early development of the zygote. Involved in the regulation of gametic DNA demethylation by inducing the conversion of the modified genomic base 5- methylcytosine (5mC) into 5-hydroxymethylcytosine (5hmC). {ECO:0000250|UniProtKB:Q9DAG5}.;
Intolerance Scores
- RVIS EVS
- 1.19
- RVIS percentile EVS
- 92.89
Essentials
- Essential (gene trap)
- N