IGFBP3
insulin like growth factor binding protein 3, the group of Insulin like growth factor binding proteins
Basic information
Region (hg38): 7:45912245-45921874
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 IGFBP3 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 | 1 | |||||
| missense | 11 | 12 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 2 |
Variants in IGFBP3
This is a list of pathogenic ClinVar variants found in the IGFBP3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-45914845-T-G | not specified | Uncertain significance (Dec 13, 2022) | ||
| 7-45914920-C-T | not specified | Uncertain significance (Jul 13, 2021) | ||
| 7-45916598-C-T | Benign (Jun 16, 2018) | |||
| 7-45916600-C-A | not specified | Uncertain significance (Oct 25, 2024) | ||
| 7-45916609-A-C | not specified | Uncertain significance (Jul 31, 2024) | ||
| 7-45917251-G-C | not specified | Uncertain significance (Jul 11, 2023) | ||
| 7-45917261-G-A | Benign (Jul 31, 2018) | |||
| 7-45917286-T-A | not specified | Uncertain significance (May 23, 2024) | ||
| 7-45917365-C-G | not specified | Uncertain significance (Jan 23, 2023) | ||
| 7-45917447-C-T | Benign (Dec 31, 2019) | |||
| 7-45920741-G-A | not specified | Uncertain significance (Aug 22, 2023) | ||
| 7-45920792-C-T | not specified | Uncertain significance (Feb 06, 2023) | ||
| 7-45920948-G-A | not specified | Uncertain significance (Sep 17, 2021) | ||
| 7-45921025-C-T | not specified | Uncertain significance (Sep 20, 2024) | ||
| 7-45921080-C-A | not specified | Uncertain significance (Sep 27, 2024) | ||
| 7-45921112-G-C | not specified | Uncertain significance (Sep 03, 2024) | ||
| 7-45921113-C-A | not specified | Uncertain significance (Nov 09, 2021) | ||
| 7-45921119-G-C | not specified | Uncertain significance (Sep 14, 2023) | ||
| 7-45921130-G-A | not specified | Uncertain significance (May 20, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IGFBP3 | protein_coding | protein_coding | ENST00000381083 | 4 | 9525 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.910 | 0.0891 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.787 | 96 | 120 | 0.798 | 0.00000720 | 1862 |
| Missense in Polyphen | 35 | 52.879 | 0.66189 | 792 | ||
| Synonymous | -0.631 | 54 | 48.4 | 1.12 | 0.00000300 | 611 |
| Loss of Function | 2.58 | 0 | 7.76 | 0.00 | 3.27e-7 | 128 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: 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. Also exhibits IGF-independent antiproliferative and apoptotic effects mediated by its receptor TMEM219/IGFBP-3R. {ECO:0000269|PubMed:20353938}.;
- Pathway
- p53 signaling pathway - Homo sapiens (human);Transcriptional misregulation in cancer - Homo sapiens (human);Cellular senescence - Homo sapiens (human);Celecoxib Pathway, Pharmacodynamics;Vitamin D Receptor Pathway;Myometrial Relaxation and Contraction Pathways;Senescence-Associated Secretory Phenotype (SASP);Photodynamic therapy-induced HIF-1 survival signaling;TP53 Regulates Transcription of Cell Death Genes;Senescence and Autophagy in Cancer;Gene expression (Transcription);hypoxia and p53 in the cardiovascular system;Generic Transcription Pathway;Post-translational protein phosphorylation;Post-translational protein modification;Metabolism of proteins;TP53 Regulates Transcription of Cell Death Genes;RNA Polymerase II Transcription;IGF signaling;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);Validated transcriptional targets of TAp63 isoforms;Transcriptional Regulation by TP53;Direct p53 effectors;Validated transcriptional targets of deltaNp63 isoforms;TP53 Regulates Transcription of Death Receptors and Ligands
(Consensus)
Recessive Scores
- pRec
- 0.822
Haploinsufficiency Scores
- pHI
- 0.289
- hipred
- Y
- hipred_score
- 0.800
- ghis
- 0.436
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.897
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Igfbp3
- Phenotype
- endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); 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; homeostasis/metabolism phenotype; limbs/digits/tail phenotype; muscle phenotype; pigmentation 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); liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); renal/urinary system phenotype; skeleton phenotype;
Zebrafish Information Network
- Gene name
- igfbp3
- Affected structure
- pharyngeal arch
- Phenotype tag
- abnormal
- Phenotype quality
- non-functional
Gene ontology
- Biological process
- regulation of cell growth;osteoblast differentiation;negative regulation of protein phosphorylation;protein phosphorylation;apoptotic process;negative regulation of cell population proliferation;negative regulation of signal transduction;regulation of glucose metabolic process;negative regulation of smooth muscle cell migration;regulation of apoptotic process;positive regulation of apoptotic process;positive regulation of MAPK cascade;regulation of insulin-like growth factor receptor signaling pathway;positive regulation of insulin-like growth factor receptor signaling pathway;regulation of phosphoprotein phosphatase activity;post-translational protein modification;cellular protein metabolic process;type B pancreatic cell proliferation;positive regulation of myoblast differentiation;negative regulation of smooth muscle cell proliferation
- Cellular component
- extracellular region;extracellular space;nucleus;endoplasmic reticulum lumen;insulin-like growth factor binding protein complex;insulin-like growth factor ternary complex
- Molecular function
- fibronectin binding;protein binding;insulin-like growth factor binding;protein tyrosine phosphatase activator activity;insulin-like growth factor I binding;insulin-like growth factor II binding;metal ion binding