TBPL2
protein-codingTATA-box binding protein like 2
Gene summary
Predicted to enable RNA polymerase II general transcription initiation factor activity. Predicted to be involved in DNA-templated transcription initiation. Located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~42.5 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 TBPL2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_199047.3. 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 | 4 | |||
| missense | 45 | 1 | 46 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 47 | 1 | 2 | 50 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_950248.2 | 7 | MANE Select | |
| Ensembl | ENSP00000247219.6 | 7 | MANE Select | |
| Ensembl | ENSP00000451597.1 | 1 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| tbpl2 | Danio rerio | Structure: trunk Quality: curvature abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Huntington,s disease - Homo sapiens (human)
- HTLV-I infection - Homo sapiens (human)
- Basal transcription factors - Homo sapiens (human)
- Viral carcinogenesis - Homo sapiens (human)
- Epstein-Barr virus infection - Homo sapiens (human)
Biological Process
- regulation of transcription by RNA polymerase II
- transcription by RNA polymerase II
- multicellular organism development
- negative regulation of transcription, DNA-templated
- RNA polymerase III preinitiation complex assembly
Molecular Function
- RNA polymerase II proximal promoter sequence-specific DNA binding
- RNA polymerase II core promoter sequence-specific DNA binding
- DNA-binding transcription factor activity, RNA polymerase II-specific
- RNA polymerase III regulatory region DNA binding
- DNA-binding transcription factor activity
Cellular Component
- transcription factor TFIIIB complex
- nucleus
- transcription factor complex
- transcription factor TFIID complex
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000247219
- Coding exons
- 7
- Length
- 43186
- Individuals with no LoFs
- 125358
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 388
- Defined
- 125748
- p
- 0.00155
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.324 | 218 | 205 | 1.06 | 0.0000107 | 2431 |
| Missense (PolyPhen) | 43 | 56.411 | 0.76227 | 710 | ||
| Synonymous | -0.285 | 84 | 80.7 | 1.04 | 0.00000453 | 758 |
| Loss of Function | 0.335 | 16 | 17.5 | 0.914 | 9.73e-7 | 198 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00092 | 0.00092 | rare |
| Latino/Admixed American | 0.00032 | 0.00032 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.013 | 0.013 | notable |
| European (Non-Finnish) | 0.00048 | 0.00046 | rare |
| South Asian | 0.000098 | 0.000098 | rare |
| Other | 0.0031 | 0.0031 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transcription factor required in complex with TAF3 for the differentiation of myoblasts into myocytes. The complex replaces TFIID at specific promoters at an early stage in the differentiation process (By similarity). {ECO:0000250|UniProtKB:Q6SJ95}.;
Recessive Scores
- pRec
- 0.113
Intolerance Scores
- LoFtool
- 0.817
- RVIS EVS
- 0.11
- RVIS percentile EVS
- 61.91
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.548
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |