IGF2BP3

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

Basic information

Region (hg38): 7:23310209-23470491

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.

not_specified (45 variants)
not_provided (1 variants)
Primary_microcephaly (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. These statistics are base on transcript: NM_000006547.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			46 clinvar			46
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	46	0	0

Loading clinvar variants...

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
Phenotype

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