IGF2BP2

insulin like growth factor 2 mRNA binding protein 2, the group of RNA binding motif containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 3:185643129-185825042

Links

ENSG00000073792 ∙ NCBI:10644 ∙ OMIM:608289 ∙ HGNC:28867 ∙ Uniprot:Q9Y6M1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• diabetes mellitus, noninsulin-dependent (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IGF2BP2 gene.

• Inborn genetic diseases (10 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGF2BP2 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		1
missense			10			10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	10	1	0

Variants in IGF2BP2

This is a list of pathogenic ClinVar variants found in the IGF2BP2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
3-185645614-G-A		not specified	Uncertain significance (Aug 02, 2021)
3-185652112-T-A			Likely benign (May 31, 2018)
3-185657366-T-A		not specified	Uncertain significance (Feb 15, 2023)
3-185658402-G-A		not specified	Uncertain significance (Feb 16, 2023)
3-185672560-G-A		not specified	Uncertain significance (Mar 13, 2023)
3-185672570-G-A		not specified	Uncertain significance (Mar 08, 2024)
3-185672579-G-A		not specified	Uncertain significance (Jun 16, 2023)
3-185672603-C-T		not specified	Uncertain significance (Jan 09, 2024)
3-185672635-C-T		not specified	Uncertain significance (Jan 02, 2024)
3-185672660-T-A		not specified	Uncertain significance (Feb 13, 2024)
3-185675352-T-C		not specified	Likely benign (Oct 27, 2023)
3-185675798-T-C		not specified	Uncertain significance (Mar 07, 2024)
3-185689361-T-C		not specified	Uncertain significance (Mar 12, 2024)
3-185689502-C-T		not specified	Uncertain significance (Oct 04, 2022)
3-185689544-G-A		not specified	Uncertain significance (Mar 24, 2023)
3-185689571-T-C		not specified	Uncertain significance (Sep 26, 2023)
3-185689590-A-G		not specified	Uncertain significance (Dec 01, 2022)
3-185692739-C-T		not specified	Uncertain significance (Apr 11, 2023)
3-185793899-G-T		Diabetes mellitus type 2, susceptibility to	risk factor (Jun 01, 2007)
3-185824915-C-T		not specified	Uncertain significance (Dec 08, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGF2BP2	protein_coding	protein_coding	ENST00000382199	16	181318

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.239	0.761	125732	0	16	125748	0.0000636

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.91	200	354	0.565	0.0000205	3905
Missense in Polyphen		62	147.87	0.41928		1746
Synonymous	0.408	136	142	0.956	0.00000914	1168
Loss of Function	4.10	8	33.7	0.237	0.00000188	374

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000906
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000881	0.0000879
Middle Eastern	0.00	0.00
South Asian	0.000101	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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 (By similarity). Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. Binding is isoform-specific. Binds to beta- actin/ACTB and MYC transcripts. {ECO:0000250, ECO:0000269|PubMed:23640942, ECO:0000269|PubMed:9891060}.
• Pathway: Metabolism of RNA;Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA (Consensus)

Recessive Scores

• pRec: 0.216

Intolerance Scores

• loftool: 0.452
• rvis_EVS: -0.76
• rvis_percentile_EVS: 13.33

Haploinsufficiency Scores

• pHI: 0.809
• hipred: Y
• hipred_score: 0.685
• ghis: 0.602

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: Igf2bp2

Gene ontology

• Biological process: anatomical structure morphogenesis;negative regulation of translation;regulation of cytokine biosynthetic process;regulation of mRNA stability;mRNA transport
• Cellular component: nucleus;cytoplasm;cytosol;cytoskeleton
• Molecular function: RNA binding;mRNA 3'-UTR binding;protein binding;translation regulator activity;mRNA 5'-UTR binding