IGFBP6

insulin like growth factor binding protein 6, the group of Insulin like growth factor binding proteins

Basic information

Region (hg38): 12:53097436-53102345

Links

ENSG00000167779 ∙ NCBI:3489 ∙ OMIM:146735 ∙ HGNC:5475 ∙ Uniprot:P24592 ∙ 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 IGFBP6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGFBP6 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					2	2
missense			20	2	2	24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	20	2	4

Variants in IGFBP6

This is a list of pathogenic ClinVar variants found in the IGFBP6 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-53097727-C-T		not specified	Likely benign (Nov 15, 2021)
12-53097746-T-C		not specified	Uncertain significance (Dec 16, 2023)
12-53097881-A-G		not specified	Uncertain significance (Feb 06, 2023)
12-53097900-G-C		not specified	Uncertain significance (Oct 13, 2021)
12-53097908-T-A		not specified	Uncertain significance (Feb 15, 2023)
12-53097932-G-A		not specified	Uncertain significance (Feb 28, 2023)
12-53097976-C-A		not specified	Uncertain significance (May 05, 2023)
12-53097979-A-G		not specified	Likely benign (Dec 10, 2024)
12-53097988-G-C		not specified	Uncertain significance (Oct 03, 2022)
12-53098034-C-A		not specified	Uncertain significance (Apr 27, 2024)
12-53098037-C-A		not specified	Uncertain significance (Feb 01, 2023)
12-53098039-C-T		not specified	Uncertain significance (Jun 06, 2023)
12-53098048-G-A		not specified	Uncertain significance (Jun 11, 2024)
12-53100760-G-A		not specified	Uncertain significance (Jan 17, 2024)
12-53100775-A-G		not specified	Uncertain significance (Jan 10, 2025)
12-53100777-C-T		not specified	Uncertain significance (Feb 22, 2023)
12-53100778-G-A		not specified	Uncertain significance (May 03, 2023)
12-53100820-C-T		not specified	Uncertain significance (Oct 05, 2023)
12-53100830-T-C			Benign (Jun 27, 2018)
12-53100836-G-A			Benign (Sep 19, 2018)
12-53100861-C-T			Likely benign (Mar 01, 2023)
12-53101050-C-T		not specified	Uncertain significance (Dec 24, 2024)
12-53101051-G-A		not specified	Uncertain significance (Dec 27, 2022)
12-53101099-G-A		not specified	Uncertain significance (Oct 01, 2024)
12-53101156-G-A			Likely benign (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGFBP6	protein_coding	protein_coding	ENST00000301464	4	4910

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0291	0.928	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.231	121	128	0.943	0.00000736	1481
Missense in Polyphen		44	51.687	0.85128		548
Synonymous	-1.40	63	50.3	1.25	0.00000251	519
Loss of Function	1.74	4	9.93	0.403	5.83e-7	95

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000231	0.000231
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000326	0.000326

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);Metabolism of proteins;IGF signaling;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) (Consensus)

Haploinsufficiency Scores

• pHI: 0.338
• hipred: N
• hipred_score: 0.287
• ghis: 0.540

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.797

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igfbp6

Gene ontology

• Biological process: regulation of cell growth;signal transduction;negative regulation of cell population proliferation;regulation of insulin-like growth factor receptor signaling pathway;cellular protein metabolic process;negative regulation of canonical Wnt signaling pathway
• Cellular component: extracellular region;extracellular space;Golgi apparatus;insulin-like growth factor binary complex
• Molecular function: fibronectin binding;signaling receptor binding;insulin-like growth factor I binding;insulin-like growth factor II binding