PHB1
prohibitin 1
Basic information
Region (hg38): 17:49404049-49414905
Previous symbols: [ "PHB" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHB1 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 2 | |||||
| Total | 0 | 0 | 4 | 1 | 4 |
Variants in PHB1
This is a list of pathogenic ClinVar variants found in the PHB1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-49404263-G-A | Breast cancer, susceptibility to | risk factor (May 19, 2001) | ||
| 17-49405058-G-A | Benign (Nov 09, 2018) | |||
| 17-49406866-G-C | Benign (Aug 17, 2019) | |||
| 17-49409096-G-A | PHB1-related disorder | Likely benign (Mar 20, 2019) | ||
| 17-49409322-T-C | PHB1-related disorder | Benign (Oct 24, 2019) | ||
| 17-49409414-G-A | not specified | Uncertain significance (Nov 06, 2023) | ||
| 17-49409447-G-A | not specified | Uncertain significance (Jun 05, 2024) | ||
| 17-49411689-G-C | not specified | Uncertain significance (Aug 21, 2023) | ||
| 17-49411726-C-A | not specified | Uncertain significance (Aug 20, 2023) | ||
| 17-49411776-C-T | not specified | Uncertain significance (Nov 08, 2022) | ||
| 17-49413201-C-T | Ovarian cancer | Benign (Jan 01, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PHB1 | protein_coding | protein_coding | ENST00000300408 | 6 | 10833 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.759 | 0.241 | 125714 | 0 | 3 | 125717 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.45 | 79 | 169 | 0.469 | 0.0000105 | 1734 |
| Missense in Polyphen | 8 | 28.398 | 0.28171 | 408 | ||
| Synonymous | 0.895 | 61 | 70.6 | 0.864 | 0.00000458 | 583 |
| Loss of Function | 2.89 | 2 | 13.4 | 0.149 | 8.06e-7 | 136 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000616 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00000886 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Prohibitin inhibits DNA synthesis. It has a role in regulating proliferation. As yet it is unclear if the protein or the mRNA exhibits this effect. May play a role in regulating mitochondrial respiration activity and in aging. {ECO:0000269|PubMed:11302691}.;
- Pathway
- Integrated Breast Cancer Pathway;RAF activation;Disease;Signal Transduction;Transport of small molecules;RAF/MAP kinase cascade;MAPK1/MAPK3 signaling;MAPK family signaling cascades;Signaling by RAS mutants;Mitochondrial calcium ion transport;Signaling by moderate kinase activity BRAF mutants;Paradoxical activation of RAF signaling by kinase inactive BRAF;Oncogenic MAPK signaling;Diseases of signal transduction;Processing of SMDT1
(Consensus)
Recessive Scores
- pRec
- 0.685
Intolerance Scores
- loftool
- 0.0551
- rvis_EVS
- 0.04
- rvis_percentile_EVS
- 56.64
Haploinsufficiency Scores
- pHI
- 0.874
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.572
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.896
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Phb
- Phenotype
- integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; endocrine/exocrine gland phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;ovarian follicle development;ovarian follicle atresia;osteoblast differentiation;regulation of transcription, DNA-templated;mitochondrial calcium ion transmembrane transport;mitochondrion organization;signal transduction;negative regulation of cell population proliferation;positive regulation of gene expression;positive regulation of cell death;negative regulation of transcription by competitive promoter binding;histone deacetylation;negative regulation of cell growth;animal organ regeneration;response to immobilization stress;negative regulation of protein catabolic process;regulation of apoptotic process;negative regulation of apoptotic process;response to peptide hormone;response to ethanol;positive regulation of G protein-coupled receptor signaling pathway;negative regulation of transcription, DNA-templated;positive regulation of transcription, DNA-templated;positive regulation of complement activation;protein stabilization;progesterone receptor signaling pathway;negative regulation of androgen receptor signaling pathway;negative regulation of ERK1 and ERK2 cascade;positive regulation of ERK1 and ERK2 cascade;cellular response to interleukin-6;DNA biosynthetic process;negative regulation of glucocorticoid receptor signaling pathway
- Cellular component
- nucleus;nucleoplasm;cytoplasm;mitochondrion;mitochondrial inner membrane;early endosome;plasma membrane;integral component of plasma membrane;cell surface;postsynaptic density;membrane;mitochondrial crista;extrinsic component of mitochondrial outer membrane;myelin sheath;extracellular exosome;extrinsic component of presynaptic active zone membrane;glutamatergic synapse;GABA-ergic synapse
- Molecular function
- DNA-binding transcription factor activity, RNA polymerase II-specific;complement component C3a binding;complement component C3b binding;protein binding;protein C-terminus binding;enzyme binding;proteinase activated receptor binding;histone deacetylase binding;transcription regulatory region DNA binding