TNP2
protein-codingtransition protein 2
Gene summary
Predicted to enable zinc ion binding activity. Predicted to be involved in several processes, including penetration of zona pellucida; positive regulation of protein processing; and sperm DNA condensation. Predicted to act upstream of or within binding activity of sperm to zona pellucida and flagellated sperm motility. Predicted to be located in chromosome and nucleolus. Predicted to be part of nucleosome. Predicted to be active in nucleus. [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 ~1.8 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 TNP2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005425.5. 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 | 1 | 1 | 2 | |||
| missense | 27 | 3 | 30 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 27 | 4 | 1 | 32 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005416.1 | 2 | MANE Select | |
| Ensembl | ENSP00000325738.3 | 2 | MANE Select | |
| Ensembl | ENSP00000496261.1 | 1 | Standard | |
| Ensembl | ENSP00000763411.1 | 1 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- multicellular organism development
- spermatogenesis
- acrosome reaction
- penetration of zona pellucida
- positive regulation of protein processing
Molecular Function
- DNA binding
- zinc ion binding
Cellular Component
- nuclear nucleosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000312693
- Coding exons
- 2
- Length
- 1786
- Individuals with no LoFs
- 123443
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 123444
- p
- 0.00000405
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.544 | 99 | 84.9 | 1.17 | 0.00000527 | 919 |
| Missense (PolyPhen) | 9 | 6.6235 | 1.3588 | 67 | ||
| Synonymous | -2.07 | 43 | 28.9 | 1.49 | 0.00000152 | 243 |
| Loss of Function | 0.286 | 3 | 3.58 | 0.837 | 1.52e-7 | 44 |
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 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a key role in the replacement of histones to protamine in the elongating spermatids of mammals. In condensing spermatids, loaded onto the nucleosomes, where it promotes the recruitment and processing of protamines, which are responsible for histone eviction. {ECO:0000250|UniProtKB:P11378}.;
Recessive Scores
- pRec
- 0.106
Intolerance Scores
- RVIS EVS
- 0.55
- RVIS percentile EVS
- 81.38
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.191
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |