HMBOX1
Basic information
Region (hg38): 8:28890395-29064764
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (23 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the HMBOX1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001135726.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 23 | 23 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 23 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| HMBOX1 | protein_coding | protein_coding | ENST00000397358 | 9 | 174371 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.998 | 0.00195 | 125733 | 0 | 4 | 125737 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.46 | 129 | 235 | 0.548 | 0.0000123 | 2766 |
| Missense in Polyphen | 40 | 96.865 | 0.41294 | 1080 | ||
| Synonymous | 1.58 | 67 | 85.5 | 0.783 | 0.00000448 | 789 |
| Loss of Function | 4.46 | 2 | 27.0 | 0.0739 | 0.00000183 | 254 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000264 | 0.0000264 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds directly to 5'-TTAGGG-3' repeats in telomeric DNA (PubMed:23813958, PubMed:23685356). Associates with the telomerase complex at sites of active telomere processing and positively regulates telomere elongation (PubMed:23685356). Important for TERT binding to chromatin, indicating a role in recruitment of the telomerase complex to telomeres (By similarity). Also plays a role in the alternative lengthening of telomeres (ALT) pathway in telomerase-negative cells where it promotes formation and/or maintenance of ALT-associated promyelocytic leukemia bodies (APBs) (PubMed:23813958). Enhances formation of telomere C-circles in ALT cells, suggesting a possible role in telomere recombination (PubMed:23813958). Might also be involved in the DNA damage response at telomeres (PubMed:23813958). {ECO:0000250|UniProtKB:Q8BJA3, ECO:0000269|PubMed:23685356, ECO:0000269|PubMed:23813958}.;
- Pathway
- miR-222 in Exercise-Induced Cardiac Growth
(Consensus)
Recessive Scores
- pRec
- 0.0942
Intolerance Scores
- loftool
- 0.0527
- rvis_EVS
- -0.34
- rvis_percentile_EVS
- 30.07
Haploinsufficiency Scores
- pHI
- 0.483
- hipred
- Y
- hipred_score
- 0.713
- ghis
- 0.596
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.341
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Hmbox1
- Phenotype
- cellular phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;positive regulation of telomere maintenance via telomerase;positive regulation of chromatin binding;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;regulation of telomerase activity;positive regulation of telomerase activity
- Cellular component
- nuclear chromosome, telomeric region;nucleus;nucleoplasm;cytoplasm;cytosol;Cajal body;nuclear body;PML body
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;double-stranded telomeric DNA binding;protein binding;telomeric DNA binding;identical protein binding;sequence-specific DNA binding;protein-containing complex binding