IGFBP2
Basic information
Region (hg38): 2:216632828-216664436
Previous symbols: [ "IBP2" ]
Links
Phenotypes
GenCC
Source:
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 IGFBP2 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 | 0 | |||||
| missense | 0 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 0 | 0 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IGFBP2 | protein_coding | protein_coding | ENST00000233809 | 4 | 31609 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.119 | 0.858 | 124710 | 0 | 3 | 124713 | 0.0000120 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.71 | 92 | 151 | 0.609 | 0.00000895 | 2021 |
| Missense in Polyphen | 24 | 58.481 | 0.41039 | 687 | ||
| Synonymous | 0.138 | 62 | 63.4 | 0.978 | 0.00000367 | 700 |
| Loss of Function | 1.95 | 3 | 9.50 | 0.316 | 4.88e-7 | 120 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000333 | 0.0000333 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000466 | 0.0000464 |
| European (Non-Finnish) | 0.00000898 | 0.00000883 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Inhibits IGF-mediated growth and developmental rates. IGF-binding proteins prolong the half-life of the IGFs and have been shown to either inhibit or stimulate the growth promoting effects of the IGFs on cell culture. They alter the interaction of IGFs with their cell surface receptors. {ECO:0000269|PubMed:19081843}.;
- Pathway
- Myometrial Relaxation and Contraction Pathways;Senescence-Associated Secretory Phenotype (SASP);Photodynamic therapy-induced HIF-1 survival signaling;Metabolism of proteins;IGF signaling;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs)
(Consensus)
Recessive Scores
- pRec
- 0.434
Haploinsufficiency Scores
- pHI
- 0.875
- hipred
- Y
- hipred_score
- 0.743
- ghis
- 0.445
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Igfbp2
- Phenotype
- immune system phenotype; renal/urinary system phenotype; liver/biliary system phenotype; hematopoietic system phenotype; 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); normal phenotype;
Gene ontology
- Biological process
- regulation of cell growth;signal transduction;female pregnancy;aging;response to nutrient;response to mechanical stimulus;response to lithium ion;response to estradiol;response to retinoic acid;cellular response to hormone stimulus;positive regulation of activated T cell proliferation;response to drug;regulation of insulin-like growth factor receptor signaling pathway;response to estrogen;cellular protein metabolic process;response to glucocorticoid;negative regulation of canonical Wnt signaling pathway
- Cellular component
- extracellular region;extracellular space;apical plasma membrane;cytoplasmic vesicle;extracellular exosome
- Molecular function
- signaling receptor binding;protein binding;insulin-like growth factor I binding;insulin-like growth factor II binding