IGFBP1

insulin like growth factor binding protein 1, the group of Insulin like growth factor binding proteins

Basic information

Region (hg38): 7:45888359-45893660

Previous symbols: [ "IBP1" ]

Links

ENSG00000146678

∙ NCBI:3484 ∙ OMIM:146730 ∙ HGNC:5469 ∙ Uniprot:P08833 ∙ 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 IGFBP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGFBP1 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			16 clinvar	1 clinvar		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in IGFBP1

This is a list of pathogenic ClinVar variants found in the IGFBP1 region.

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

Position	Phenotype	Significance	ClinVar
7-45888732-C-T	Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)	1712930
7-45888770-C-T	not specified	Uncertain significance (May 25, 2022)	2412536
7-45888829-T-G	not specified	Uncertain significance (Dec 12, 2023)	3108599
7-45888855-G-A	not specified	Uncertain significance (Nov 18, 2022)	2328025
7-45888884-T-G	Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)	1713033
7-45888894-G-T	not specified	Uncertain significance (Feb 10, 2022)	2343756
7-45888969-A-C	not specified	Likely benign (Aug 17, 2021)	2351220
7-45888975-C-T	not specified	Uncertain significance (Feb 27, 2024)	3108600
7-45888981-C-A	not specified	Uncertain significance (Dec 27, 2023)	3108601
7-45890551-C-A	not specified	Uncertain significance (Dec 21, 2023)	3108602
7-45890586-A-C	not specified	Uncertain significance (Aug 02, 2021)	2354935
7-45890671-A-G	not specified	Uncertain significance (Oct 27, 2023)	3108603
7-45890680-C-T	not specified	Uncertain significance (Dec 20, 2022)	2337636
7-45891962-G-A	not specified	Uncertain significance (Oct 28, 2023)	3108604
7-45892000-A-T	not specified	Likely benign (Jun 02, 2024)	3285529
7-45892973-T-C	not specified	Uncertain significance (Feb 15, 2023)	2484757
7-45893035-T-A	not specified	Uncertain significance (Jan 30, 2024)	3108605
7-45893038-C-G	not specified	Uncertain significance (Aug 02, 2021)	2240582
7-45893046-C-G	not specified	Uncertain significance (Oct 20, 2023)	3108607
7-45893051-G-T	not specified	Uncertain significance (Feb 28, 2024)	3108608

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGFBP1	protein_coding	protein_coding	ENST00000275525	4	5312

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000947	0.821	125718	0	11	125729	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.253	125	133	0.938	0.00000643	1634
Missense in Polyphen		38	44.34	0.85701		586
Synonymous	-0.216	60	57.9	1.04	0.00000304	524
Loss of Function	1.15	6	9.92	0.605	5.02e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000620	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000585	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000585	0.0000544
South Asian	0.000247	0.000229
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. Promotes cell migration. {ECO:0000269|PubMed:15972819}.;
Pathway: IGF-Ncore;ATF4 activates genes;Aryl Hydrocarbon Receptor Pathway;Vitamin D Receptor Pathway;Nuclear Receptors Meta-Pathway;Myometrial Relaxation and Contraction Pathways;Senescence-Associated Secretory Phenotype (SASP);Photodynamic therapy-induced HIF-1 survival signaling;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);HIF-1-alpha transcription factor network;FOXA2 and FOXA3 transcription factor networks (Consensus)

Recessive Scores

pRec: 0.747

Haploinsufficiency Scores

pHI: 0.600
hipred: N
hipred_score: 0.258
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.997

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Igfbp1
Phenotype: immune system phenotype; liver/biliary system phenotype; cellular phenotype;

Gene ontology

Biological process: signal transduction;aging;insulin receptor signaling pathway;positive regulation of cell growth;PERK-mediated unfolded protein response;tissue regeneration;regulation of insulin-like growth factor receptor signaling pathway;post-translational protein modification;cellular protein metabolic process;negative regulation of canonical Wnt signaling pathway
Cellular component: extracellular region;extracellular space;endoplasmic reticulum lumen;Golgi apparatus
Molecular function: signaling receptor binding;protein binding;insulin-like growth factor binding;insulin-like growth factor I binding;insulin-like growth factor II binding