IGFBP4

insulin like growth factor binding protein 4, the group of Insulin like growth factor binding proteins

Basic information

Region (hg38): 17:40443450-40457725

Links

ENSG00000141753 ∙ NCBI:3487 ∙ OMIM:146733 ∙ HGNC:5473 ∙ Uniprot:P22692 ∙ 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 IGFBP4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGFBP4 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	2
missense		1	8	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	8	2	1

Variants in IGFBP4

This is a list of pathogenic ClinVar variants found in the IGFBP4 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-40443853-C-T		not specified	Uncertain significance (Jul 14, 2021)
17-40443859-G-T		not specified	Uncertain significance (Nov 20, 2023)
17-40443868-G-C		not specified	Uncertain significance (Sep 25, 2023)
17-40444070-G-C		not specified	Uncertain significance (Jan 17, 2023)
17-40452992-C-T			Benign (Mar 29, 2018)
17-40453006-C-G		not specified	Uncertain significance (Dec 21, 2023)
17-40453010-C-T			Likely benign (Nov 01, 2022)
17-40453057-A-G		not specified	Uncertain significance (Aug 08, 2023)
17-40453135-G-A			Likely benign (May 01, 2022)
17-40453962-C-T		not specified	Uncertain significance (Dec 15, 2023)
17-40453970-C-T		not specified	Uncertain significance (Dec 27, 2023)
17-40456504-C-T		Abnormal brain morphology	Likely pathogenic (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGFBP4	protein_coding	protein_coding	ENST00000269593	4	14282

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0231	0.919	125733	0	4	125737	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.854	117	146	0.801	0.00000903	1621
Missense in Polyphen		44	66.201	0.66465		661
Synonymous	1.38	47	60.7	0.775	0.00000355	519
Loss of Function	1.62	4	9.34	0.428	4.67e-7	102

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000316	0.0000316
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• 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: Myometrial Relaxation and Contraction Pathways;Senescence-Associated Secretory Phenotype (SASP);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);Wnt signaling network (Consensus)

Recessive Scores

• pRec: 0.350

Haploinsufficiency Scores

• pHI: 0.575
• hipred: Y
• hipred_score: 0.666
• ghis: 0.630

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.829

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igfbp4
• 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); muscle phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: skeletal system development;regulation of cell growth;DNA metabolic process;inflammatory response;signal transduction;cell population proliferation;regulation of glucose metabolic process;positive regulation of MAPK cascade;regulation of insulin-like growth factor receptor signaling pathway;positive 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 canonical Wnt signaling pathway
• Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen
• Molecular function: signaling receptor binding;protein binding;insulin-like growth factor I binding;insulin-like growth factor II binding