IGF2BP1
insulin like growth factor 2 mRNA binding protein 1, the group of RNA binding motif containing
Basic information
Region (hg38): 17:48997385-49056145
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 IGF2BP1 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 | 22 | 23 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 1 | |||||
| Total | 0 | 0 | 22 | 1 | 3 |
Variants in IGF2BP1
This is a list of pathogenic ClinVar variants found in the IGF2BP1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 17-48999106-T-C | Benign (Jul 30, 2018) | |||
| 17-48999124-A-G | not specified | Uncertain significance (Nov 21, 2024) | ||
| 17-48999165-C-A | not specified | Uncertain significance (Nov 15, 2021) | ||
| 17-49026498-A-G | Benign/Likely benign (Dec 01, 2022) | |||
| 17-49038204-C-A | not specified | Uncertain significance (Apr 29, 2024) | ||
| 17-49038272-G-A | not specified | Uncertain significance (Jul 27, 2024) | ||
| 17-49038313-G-C | not specified | Uncertain significance (Sep 12, 2023) | ||
| 17-49038329-C-T | not specified | Uncertain significance (Jul 11, 2022) | ||
| 17-49038421-C-T | not specified | Uncertain significance (Mar 23, 2023) | ||
| 17-49038433-A-G | not specified | Uncertain significance (Apr 23, 2024) | ||
| 17-49039981-C-T | Benign (Jul 16, 2018) | |||
| 17-49040021-C-T | not specified | Uncertain significance (Jan 04, 2022) | ||
| 17-49040068-T-A | Benign (Feb 01, 2024) | |||
| 17-49041379-G-T | not specified | Uncertain significance (Apr 25, 2023) | ||
| 17-49041385-G-A | not specified | Uncertain significance (Jan 29, 2024) | ||
| 17-49041434-T-C | not specified | Uncertain significance (Jun 09, 2022) | ||
| 17-49042297-A-G | not specified | Uncertain significance (Mar 29, 2022) | ||
| 17-49042310-G-A | not specified | Uncertain significance (Jun 25, 2024) | ||
| 17-49042318-G-A | not specified | Uncertain significance (Dec 02, 2022) | ||
| 17-49042331-T-C | not specified | Uncertain significance (Oct 03, 2022) | ||
| 17-49042342-C-T | not specified | Uncertain significance (Jan 20, 2023) | ||
| 17-49042369-G-C | not specified | Uncertain significance (Dec 23, 2022) | ||
| 17-49042376-G-A | not specified | Uncertain significance (Jan 16, 2024) | ||
| 17-49043494-G-A | not specified | Uncertain significance (Mar 20, 2024) | ||
| 17-49043504-C-A | not specified | Uncertain significance (Feb 10, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| IGF2BP1 | protein_coding | protein_coding | ENST00000290341 | 15 | 58239 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.999 | 0.000667 | 125734 | 0 | 2 | 125736 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.52 | 165 | 350 | 0.471 | 0.0000202 | 3781 |
| Missense in Polyphen | 30 | 114.23 | 0.26264 | 1255 | ||
| Synonymous | 0.732 | 125 | 136 | 0.920 | 0.00000820 | 1125 |
| Loss of Function | 4.95 | 3 | 34.3 | 0.0874 | 0.00000211 | 356 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000617 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). This transcript 'caging' into mRNPs allows mRNA transport and transient storage. It also modulates the rate and location at which target transcripts encounter the translational apparatus and shields them from endonuclease attacks or microRNA-mediated degradation. Plays a direct role in the transport and translation of transcripts required for axonal regeneration in adult sensory neurons (By similarity). Regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. Co-transcriptionally associates with the ACTB mRNA in the nucleus. This binding involves a conserved 54-nucleotide element in the ACTB mRNA 3'-UTR, known as the 'zipcode'. The RNP thus formed is exported to the cytoplasm, binds to a motor protein and is transported along the cytoskeleton to the cell periphery. During transport, prevents ACTB mRNA from being translated into protein. When the RNP complex reaches its destination near the plasma membrane, IGF2BP1 is phosphorylated. This releases the mRNA, allowing ribosomal 40S and 60S subunits to assemble and initiate ACTB protein synthesis. Monomeric ACTB then assembles into the subcortical actin cytoskeleton (By similarity). During neuronal development, key regulator of neurite outgrowth, growth cone guidance and neuronal cell migration, presumably through the spatiotemporal fine tuning of protein synthesis, such as that of ACTB (By similarity). May regulate mRNA transport to activated synapses (By similarity). Binds to and stabilizes ABCB1/MDR-1 mRNA (By similarity). During interstinal wound repair, interacts with and stabilizes PTGS2 transcript. PTGS2 mRNA stabilization may be crucial for colonic mucosal wound healing (By similarity). Binds to the 3'-UTR of IGF2 mRNA by a mechanism of cooperative and sequential dimerization and regulates IGF2 mRNA subcellular localization and translation. Binds to MYC mRNA, in the coding region instability determinant (CRD) of the open reading frame (ORF), hence prevents MYC cleavage by endonucleases and possibly microRNA targeting to MYC-CRD. Binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. Binds to the oncofetal H19 transcript and to the neuron-specific TAU mRNA and regulates their localizations. Binds to and stabilizes BTRC/FBW1A mRNA. Binds to the adenine-rich autoregulatory sequence (ARS) located in PABPC1 mRNA and represses its translation. PABPC1 mRNA-binding is stimulated by PABPC1 protein. Prevents BTRC/FBW1A mRNA degradation by disrupting microRNA-dependent interaction with AGO2. Promotes the directed movement of tumor-derived cells by fine-tuning intracellular signaling networks. Binds to MAPK4 3'-UTR and inhibits its translation. Interacts with PTEN transcript open reading frame (ORF) and prevents mRNA decay. This combined action on MAPK4 (down-regulation) and PTEN (up-regulation) antagonizes HSPB1 phosphorylation, consequently it prevents G-actin sequestration by phosphorylated HSPB1, allowing F-actin polymerization. Hence enhances the velocity of cell migration and stimulates directed cell migration by PTEN-modulated polarization. Interacts with Hepatitis C virus (HCV) 5'-UTR and 3'-UTR and specifically enhances translation at the HCV IRES, but not 5'-cap- dependent translation, possibly by recruiting eIF3. Interacts with HIV-1 GAG protein and blocks the formation of infectious HIV-1 particles. Reduces HIV-1 assembly by inhibiting viral RNA packaging, as well as assembly and processing of GAG protein on cellular membranes. During cellular stress, such as oxidative stress or heat shock, stabilizes target mRNAs that are recruited to stress granules, including CD44, IGF2, MAPK4, MYC, PTEN, RAPGEF2 and RPS6KA5 transcripts. {ECO:0000250, ECO:0000269|PubMed:10875929, ECO:0000269|PubMed:16356927, ECO:0000269|PubMed:16541107, ECO:0000269|PubMed:16778892, ECO:0000269|PubMed:17101699, ECO:0000269|PubMed:17255263, ECO:0000269|PubMed:17893325, ECO:0000269|PubMed:18385235, ECO:0000269|PubMed:19029303, ECO:0000269|PubMed:19541769, ECO:0000269|PubMed:19647520, ECO:0000269|PubMed:20080952, ECO:0000269|PubMed:22279049, ECO:0000269|PubMed:8132663, ECO:0000269|PubMed:9891060}.;
- Pathway
- MicroRNAs in cancer - Homo sapiens (human);miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Brain-Derived Neurotrophic Factor (BDNF) signaling pathway;eIF5A regulation in response to inhibition of the nuclear export system;Signal Transduction;MAPK6/MAPK4 signaling;Metabolism of RNA;Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA;MAPK family signaling cascades;Regulation of nuclear beta catenin signaling and target gene transcription
(Consensus)
Recessive Scores
- pRec
- 0.488
Intolerance Scores
- loftool
- 0.187
- rvis_EVS
- -0.38
- rvis_percentile_EVS
- 27.69
Haploinsufficiency Scores
- pHI
- 0.923
- hipred
- Y
- hipred_score
- 0.880
- ghis
- 0.485
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.868
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Igf2bp1
- Phenotype
- immune system phenotype; skeleton phenotype; renal/urinary system phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary 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); hematopoietic system phenotype; neoplasm; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; cellular phenotype; homeostasis/metabolism phenotype; muscle phenotype; craniofacial phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype;
Zebrafish Information Network
- Gene name
- igf2bp1
- Affected structure
- optic tectum
- Phenotype tag
- abnormal
- Phenotype quality
- has fewer parts of type
Gene ontology
- Biological process
- regulation of mRNA stability involved in response to stress;negative regulation of translation;pallium cell proliferation in forebrain;regulation of cytokine biosynthetic process;regulation of mRNA stability;mRNA transport;CRD-mediated mRNA stabilization;neuronal stem cell population maintenance
- Cellular component
- nucleoplasm;cytoplasm;cytosol;cytoplasmic stress granule;lamellipodium;filopodium;growth cone;dendritic spine;perinuclear region of cytoplasm;CRD-mediated mRNA stability complex;ribonucleoprotein complex
- Molecular function
- RNA binding;mRNA binding;mRNA 3'-UTR binding;protein binding;translation regulator activity;mRNA 5'-UTR binding