PPARGC1B
PPARG coactivator 1 beta, the group of RNA binding motif containing|MicroRNA protein coding host genes
Basic information
Region (hg38): 5:149730298-149855022
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (174 variants)
- not_provided (15 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the PPARGC1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000133263.4. 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 | 4 | |||||
| missense | 166 | 182 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 166 | 9 | 11 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| PPARGC1B | protein_coding | protein_coding | ENST00000309241 | 12 | 124725 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.503 | 0.497 | 125726 | 0 | 22 | 125748 | 0.0000875 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.503 | 566 | 601 | 0.942 | 0.0000362 | 6582 |
| Missense in Polyphen | 143 | 164.58 | 0.86888 | 1848 | ||
| Synonymous | -0.985 | 274 | 254 | 1.08 | 0.0000158 | 2080 |
| Loss of Function | 4.89 | 10 | 45.7 | 0.219 | 0.00000254 | 499 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000387 | 0.000304 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000981 | 0.0000924 |
| European (Non-Finnish) | 0.000109 | 0.000105 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000667 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role of stimulator of transcription factors and nuclear receptors activities. Activates transcriptional activity of estrogen receptor alpha, nuclear respiratory factor 1 (NRF1) and glucocorticoid receptor in the presence of glucocorticoids. May play a role in constitutive non-adrenergic-mediated mitochondrial biogenesis as suggested by increased basal oxygen consumption and mitochondrial number when overexpressed. May be involved in fat oxidation and non-oxidative glucose metabolism and in the regulation of energy expenditure. Induces the expression of PERM1 in the skeletal muscle in an ESRRA-dependent manner. {ECO:0000269|PubMed:11854298, ECO:0000269|PubMed:12678921, ECO:0000269|PubMed:15546003, ECO:0000269|PubMed:23836911}.;
- Pathway
- Insulin resistance - Homo sapiens (human);AMP-activated Protein Kinase (AMPK) Signaling;Energy Metabolism;Sterol Regulatory Element-Binding Proteins (SREBP) signalling;Differentiation of white and brown adipocyte;Mitochondrial Gene Expression;Sudden Infant Death Syndrome (SIDS) Susceptibility Pathways;Prostaglandin Synthesis and Regulation;Transcriptional regulation by RUNX2;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Transcriptional activation of mitochondrial biogenesis;Mitochondrial biogenesis;Regulation of RUNX2 expression and activity;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.214
Intolerance Scores
- loftool
- 0.489
- rvis_EVS
- 1.06
- rvis_percentile_EVS
- 91.47
Haploinsufficiency Scores
- pHI
- 0.234
- hipred
- Y
- hipred_score
- 0.594
- ghis
- 0.430
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.846
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ppargc1b
- Phenotype
- adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region phenotype; muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system 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); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; skeleton phenotype;
Gene ontology
- Biological process
- ossification;regulation of transcription, DNA-templated;mitochondrial transcription;actin filament organization;positive regulation of alkaline phosphatase activity;intracellular estrogen receptor signaling pathway;cellular response to reactive oxygen species;positive regulation of phosphorylation;positive regulation of osteoclast differentiation;positive regulation of bone resorption;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of DNA-binding transcription factor activity;response to glucocorticoid;response to cAMP;bone trabecula formation;positive regulation of cold-induced thermogenesis
- Cellular component
- nucleus;nucleoplasm;mitochondrion;mediator complex
- Molecular function
- transcription coregulator activity;RNA binding;transcription factor binding;estrogen receptor binding;nuclear receptor transcription coactivator activity;AF-2 domain binding