HBP1
protein-codingHMG-box transcription factor 1
Gene summary
Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in negative regulation of lipid transport; negative regulation of reactive oxygen species biosynthetic process; and negative regulation of transcription by RNA polymerase II. Located in nuclear speck. Biomarker of osteoarthritis. [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 ~33.6 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 HBP1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_012257.4. 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 | 0 | |||||
| missense | 54 | 54 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 60 | 0 | 0 | 60 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_036389.2 | 10 | MANE Select | |
| Ensembl | ENSP00000222574.4 | 10 | MANE Select | |
| RefSeq | NP_001231191.1 | 11 | Standard | |
| RefSeq | NP_001425940.1 | 10 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Validated transcriptional targets of TAp63 isoforms
- C-MYC pathway
- Regulation of nuclear beta catenin signaling and target gene transcription
- Signaling mediated by p38-alpha and p38-beta
- Validated transcriptional targets of deltaNp63 isoforms
Biological Process
- regulation of transcription by RNA polymerase II
- cell cycle arrest
- Wnt signaling pathway
Molecular Function
- DNA-binding transcription factor activity, RNA polymerase II-specific
- DNA binding
- RNA binding
- protein binding
Cellular Component
- nucleoplasm
- nuclear speck
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000222574
- Coding exons
- 10
- Length
- 33569
- Individuals with no LoFs
- 125634
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 107
- Defined
- 125742
- p
- 0.000430
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.64 | 197 | 273 | 0.721 | 0.0000133 | 3390 |
| Missense (PolyPhen) | 39 | 110.42 | 0.35319 | 1346 | ||
| Synonymous | -0.986 | 106 | 93.8 | 1.13 | 0.00000452 | 928 |
| Loss of Function | 3.17 | 9 | 26.6 | 0.338 | 0.00000123 | 348 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0055 | 0.0052 | notable |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000098 | 0.000088 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transcriptional repressor that binds to the promoter region of target genes. Plays a role in the regulation of the cell cycle and of the Wnt pathway. Binds preferentially to the sequence 5'-TTCATTCATTCA-3'. Binding to the H1F0 promoter is enhanced by interaction with RB1. Disrupts the interaction between DNA and TCF4. {ECO:0000269|PubMed:10562551, ECO:0000269|PubMed:10958660, ECO:0000269|PubMed:11500377}.;
Recessive Scores
- pRec
- 0.166
Intolerance Scores
- LoFtool
- 0.218
- RVIS EVS
- -0.32
- RVIS percentile EVS
- 31.69
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.999
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |