IGFBP5

insulin like growth factor binding protein 5, the group of Insulin like growth factor binding proteins

Basic information

Region (hg38): 2:216672105-216695549

Links

ENSG00000115461

∙ NCBI:3488 ∙ OMIM:146734 ∙ HGNC:5474 ∙ Uniprot:P24593 ∙ 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 IGFBP5 gene.

not_specified (37 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGFBP5 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000000599.4. 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			3 clinvar	1 clinvar		4
missense			40 clinvar			40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	44	1	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGFBP5	protein_coding	protein_coding	ENST00000233813	4	23421

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.963	0.0371	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.63	97	154	0.630	0.00000943	1743
Missense in Polyphen		28	57.346	0.48826		624
Synonymous	0.332	53	56.2	0.944	0.00000307	520
Loss of Function	2.97	0	10.3	0.00	4.38e-7	135

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)	0.00	0.00
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: Vitamin D Receptor Pathway;Myometrial Relaxation and Contraction Pathways;Senescence-Associated Secretory Phenotype (SASP);Factors and pathways affecting insulin-like growth factor (IGF1)-Akt signaling;Senescence and Autophagy in Cancer;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) (Consensus)

Recessive Scores

pRec: 0.319

Haploinsufficiency Scores

pHI: 0.659
hipred: Y
hipred_score: 0.809
ghis: 0.562

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.763

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Igfbp5
Phenotype: homeostasis/metabolism phenotype; muscle 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); growth/size/body region phenotype;

Gene ontology

Biological process: regulation of cell growth;osteoblast differentiation;glucose metabolic process;signal transduction;female pregnancy;aging;regulation of glucose metabolic process;negative regulation of smooth muscle cell migration;negative regulation of translation;negative regulation of cell migration;hair follicle morphogenesis;intracellular signal transduction;glucose homeostasis;regulation of insulin-like growth factor receptor signaling pathway;positive regulation of insulin-like growth factor receptor signaling pathway;negative 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 osteoblast differentiation;negative regulation of growth;lung alveolus development;negative regulation of smooth muscle cell proliferation;striated muscle cell differentiation;positive regulation of protein kinase B signaling;mammary gland involution;response to growth hormone;cellular response to cAMP;cellular response to organic cyclic compound;negative regulation of muscle tissue development;negative regulation of skeletal muscle hypertrophy;positive regulation of vascular smooth muscle cell proliferation;positive regulation of vascular associated smooth muscle cell migration
Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen;insulin-like growth factor binding protein complex;insulin-like growth factor ternary complex
Molecular function: fibronectin binding;protein binding;insulin-like growth factor I binding;insulin-like growth factor II binding