IGF2BP3

insulin like growth factor 2 mRNA binding protein 3, the group of RNA binding motif containing

Basic information

Region (hg38): 7:23310208-23470491

Links

ENSG00000136231 ∙ NCBI:10643 ∙ OMIM:608259 ∙ HGNC:28868 ∙ Uniprot:O00425 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the IGF2BP3 gene.

• Inborn genetic diseases (18 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGF2BP3 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding			1			1
Total	0	0	18	0	0

Variants in IGF2BP3

This is a list of pathogenic ClinVar variants found in the IGF2BP3 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-23312812-C-T		not specified	Uncertain significance (Jul 14, 2021)
7-23313523-G-A		not specified	Uncertain significance (Feb 17, 2022)
7-23319261-G-T			Benign (Feb 08, 2018)
7-23342074-G-A		not specified	Uncertain significance (Aug 16, 2022)
7-23342154-G-C		not specified	Uncertain significance (Dec 12, 2023)
7-23343774-C-T		not specified	Uncertain significance (Feb 10, 2022)
7-23345959-T-C		Primary microcephaly	Uncertain significance (Dec 01, 2020)
7-23345961-T-C		not specified	Uncertain significance (Nov 08, 2022)
7-23345970-T-C		not specified	Uncertain significance (Feb 15, 2023)
7-23346020-A-C		not specified	Uncertain significance (Dec 07, 2021)
7-23347645-T-C		not specified	Uncertain significance (Jan 31, 2023)
7-23347708-G-A		not specified	Uncertain significance (Aug 10, 2021)
7-23347720-C-T		not specified	Uncertain significance (Jul 26, 2022)
7-23351378-T-C		not specified	Uncertain significance (Dec 07, 2021)
7-23351426-C-T		not specified	Uncertain significance (Aug 13, 2021)
7-23351471-C-A		not specified	Uncertain significance (Mar 02, 2023)
7-23351476-C-T		not specified	Uncertain significance (Jan 09, 2024)
7-23396808-G-A		Vascular endothelial growth factor (VEGF) inhibitor response	association (-)
7-23418792-G-C		not specified	Uncertain significance (May 05, 2023)
7-23418811-G-C		not specified	Uncertain significance (Apr 18, 2023)
7-23418817-T-G		not specified	Uncertain significance (Jan 30, 2024)
7-23468516-T-C		not specified	Uncertain significance (Feb 23, 2023)
7-23469972-C-T		not specified	Uncertain significance (May 16, 2023)
7-23469977-G-A		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGF2BP3	protein_coding	protein_coding	ENST00000258729	15	160259

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000140	125743	0	5	125748	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.12	218	325	0.670	0.0000173	3753
Missense in Polyphen		35	90.72	0.3858		1041
Synonymous	-0.743	128	118	1.09	0.00000612	1132
Loss of Function	5.20	0	31.4	0.00	0.00000152	387

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)	0.0000443	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: RNA-binding factor that may recruit 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. Binds to the 3'-UTR of CD44 mRNA and stabilizes it, hence promotes cell adhesion and invadopodia formation in cancer cells. Binds to beta- actin/ACTB and MYC transcripts. Binds to the 5'-UTR of the insulin-like growth factor 2 (IGF2) mRNAs. {ECO:0000269|PubMed:16541107, ECO:0000269|PubMed:23640942}.
• Pathway: Metabolism of RNA;Insulin-like Growth Factor-2 mRNA Binding Proteins (IGF2BPs/IMPs/VICKZs) bind RNA (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.0612
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.43

Haploinsufficiency Scores

• pHI: 0.812
• hipred: Y
• hipred_score: 0.703
• ghis: 0.457

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.851

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Igf2bp3

Gene ontology

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