TFPT
protein-codingTCF3 fusion partner, the group of INO80 complex
Gene summary
Predicted to enable DNA binding activity and protein kinase binding activity. Involved in several processes, including apoptotic signaling pathway; positive regulation of DNA-templated transcription; and regulation of DNA metabolic process. Located in nucleoplasm. Part of Ino80 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 ~8.6 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 TFPT variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_013342.4. 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 | 2 | 2 | ||||
| missense | 54 | 54 | ||||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 58 | 0 | 0 | 58 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_037474.1 | 6 | MANE Select | |
| Ensembl | ENSP00000375639.1 | 6 | MANE Select | |
| RefSeq | NP_001308721.1 | 5 | Standard | |
| Ensembl | ENSP00000375637.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- DNA Repair
- Post-translational protein modification
- Metabolism of proteins
- UCH proteinases
- Deubiquitination
Biological Process
- DNA repair
- DNA recombination
- apoptotic process
- protein deubiquitination
- apoptotic signaling pathway
Molecular Function
- DNA binding
- protein binding
Cellular Component
- nucleus
- nucleoplasm
- cytoplasm
- Ino80 complex
- nuclear membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000391759
- Coding exons
- 6
- Length
- 8736
- Individuals with no LoFs
- 125718
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 30
- Defined
- 125748
- p
- 0.000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.462 | 146 | 163 | 0.898 | 0.0000102 | 1582 |
| Missense (PolyPhen) | 25 | 33.126 | 0.75469 | 415 | ||
| Synonymous | -0.521 | 72 | 66.6 | 1.08 | 0.00000374 | 555 |
| Loss of Function | 1.25 | 8 | 12.9 | 0.622 | 7.17e-7 | 137 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.00033 | 0.00032 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00023 | 0.00022 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000064 | 0.000053 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Appears to promote apoptosis in a p53/TP53-independent manner.;
- Disease
- DISEASE: Note=A chromosomal aberration involving TFPT is a cause of pre-B-cell acute lymphoblastic leukemia (B-ALL). Inversion inv(19)(p13;q13) with TCF3. {ECO:0000269|PubMed:10086727}.;
Recessive Scores
- pRec
- 0.271
Intolerance Scores
- LoFtool
- 0.306
- RVIS EVS
- -0.14
- RVIS percentile EVS
- 43.57
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- S
- Essential (gene trap)
- K
- Indispensability pred.
- E
- Indispensability score
- 0.991
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |