IGFBP5
Basic information
Region (hg38): 2:216672105-216695549
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 IGFBP5 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 | 12 | 12 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 12 | 0 | 0 |
Variants in IGFBP5
This is a list of pathogenic ClinVar variants found in the IGFBP5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
2-216676760-G-A | EBV-positive nodal T- and NK-cell lymphoma | Likely benign (-) | ||
2-216676808-C-A | not specified | Uncertain significance (May 08, 2024) | ||
2-216678159-C-T | not specified | Uncertain significance (Jun 07, 2024) | ||
2-216678165-G-A | not specified | Uncertain significance (Oct 25, 2024) | ||
2-216678878-G-A | not specified | Uncertain significance (Nov 09, 2024) | ||
2-216678890-C-T | not specified | Uncertain significance (Dec 26, 2023) | ||
2-216678909-C-T | not specified | Uncertain significance (Aug 04, 2023) | ||
2-216678950-C-T | not specified | Uncertain significance (May 29, 2024) | ||
2-216678981-C-T | not specified | Uncertain significance (Aug 02, 2021) | ||
2-216678989-C-T | not specified | Uncertain significance (May 23, 2024) | ||
2-216679004-C-T | not specified | Uncertain significance (Mar 07, 2024) | ||
2-216679006-G-T | not specified | Uncertain significance (Jul 19, 2023) | ||
2-216679009-G-C | not specified | Uncertain significance (Aug 15, 2023) | ||
2-216694490-C-T | not specified | Uncertain significance (Aug 28, 2023) | ||
2-216694658-G-C | not specified | Uncertain significance (Aug 08, 2023) | ||
2-216694661-G-A | not specified | Uncertain significance (May 24, 2023) | ||
2-216694687-C-G | not specified | Uncertain significance (Nov 22, 2024) | ||
2-216694704-G-C | not specified | Uncertain significance (Nov 15, 2024) | ||
2-216694726-G-C | not specified | Uncertain significance (Jan 31, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
IGFBP5 | protein_coding | protein_coding | ENST00000233813 | 4 | 23421 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.963 | 0.0371 | 0 | 0 | 0 | 0 | 0.00 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.63 | 97 | 154 | 0.630 | 0.00000943 | 1743 |
Missense in Polyphen | 28 | 57.346 | 0.48826 | 624 | ||
Synonymous | 0.332 | 53 | 56.2 | 0.944 | 0.00000307 | 520 |
Loss of Function | 2.97 | 0 | 10.3 | 0.00 | 4.38e-7 | 135 |
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.;
- Pathway
- Vitamin D Receptor Pathway;Myometrial Relaxation and Contraction Pathways;Senescence-Associated Secretory Phenotype (SASP);Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling;Senescence and Autophagy in Cancer;Post-translational protein phosphorylation;Post-translational protein modification;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
- 0.319
Haploinsufficiency Scores
- pHI
- 0.659
- hipred
- Y
- hipred_score
- 0.809
- ghis
- 0.562
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.763
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Igfbp5
- Phenotype
- homeostasis/metabolism phenotype; muscle 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); growth/size/body region phenotype;
Gene ontology
- Biological process
- regulation of cell growth;osteoblast differentiation;glucose metabolic process;signal transduction;female pregnancy;aging;regulation of glucose metabolic process;negative regulation of smooth muscle cell migration;negative regulation of translation;negative regulation of cell migration;hair follicle morphogenesis;intracellular signal transduction;glucose homeostasis;regulation of insulin-like growth factor receptor signaling pathway;positive regulation of insulin-like growth factor receptor signaling pathway;negative regulation of insulin-like growth factor receptor signaling pathway;post-translational protein modification;cellular protein metabolic process;type B pancreatic cell proliferation;negative regulation of osteoblast differentiation;negative regulation of growth;lung alveolus development;negative regulation of smooth muscle cell proliferation;striated muscle cell differentiation;positive regulation of protein kinase B signaling;mammary gland involution;response to growth hormone;cellular response to cAMP;cellular response to organic cyclic compound;negative regulation of muscle tissue development;negative regulation of skeletal muscle hypertrophy;positive regulation of vascular smooth muscle cell proliferation;positive regulation of vascular associated smooth muscle cell migration
- Cellular component
- extracellular region;extracellular space;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 I binding;insulin-like growth factor II binding