IGF2R

insulin like growth factor 2 receptor, the group of CD molecules|MRH domain containing

Basic information

Region (hg38): 6:159969081-160113507

Links

ENSG00000197081 ∙ NCBI:3482 ∙ OMIM:147280 ∙ HGNC:5467 ∙ Uniprot:P11717 ∙ 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 IGF2R gene.

• Inborn genetic diseases (79 variants)
• not provided (31 variants)
• Hepatocellular carcinoma (3 variants)
• not specified (1 variants)
• Premature ovarian failure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGF2R 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	13	5	19
missense		1	72	10	9	92
nonsense						0
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding						0
Total	0	2	73	23	14

Highest pathogenic variant AF is 0.00000658

Variants in IGF2R

This is a list of pathogenic ClinVar variants found in the IGF2R region.

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

Position	Type	Phenotype	Significance	ClinVar
6-159969289-CCCGCCCG-C		Hepatocellular carcinoma	Likely pathogenic (May 03, 2020)
6-159969296-G-C		Hepatocellular carcinoma	Uncertain significance (Mar 09, 2021)
6-159969298-C-T		not specified	Uncertain significance (Dec 20, 2023)
6-159969361-C-G		not specified	Uncertain significance (Dec 26, 2023)
6-159991230-A-G		not specified	Uncertain significance (Mar 14, 2023)
6-159991243-G-A		not specified	Uncertain significance (Dec 22, 2023)
6-159991254-A-G		not specified	Likely benign (Oct 05, 2022)
6-159991281-G-A		not specified	Uncertain significance (Jun 27, 2022)
6-160009030-G-A		not specified	Uncertain significance (Jan 06, 2023)
6-160009072-G-A		not specified	Uncertain significance (Feb 06, 2023)
6-160009093-A-G		not specified	Uncertain significance (Jan 17, 2024)
6-160009133-T-A		Hepatocellular carcinoma	Pathogenic (Jun 15, 2021)
6-160010723-C-T		Premature ovarian failure	Likely pathogenic (Mar 02, 2020)
6-160010747-G-A		not specified	Uncertain significance (May 11, 2022)
6-160010748-C-A		not specified	Uncertain significance (Aug 08, 2022)
6-160024661-C-T			Likely benign (Jun 01, 2022)
6-160024662-G-C		not specified	Uncertain significance (Sep 17, 2021)
6-160024672-C-T		not specified	Uncertain significance (Oct 18, 2021)
6-160027224-C-G		not specified	Uncertain significance (Aug 12, 2021)
6-160027232-A-G			Benign (Jul 23, 2018)
6-160027261-G-T		not specified	Uncertain significance (Aug 17, 2022)
6-160027264-G-A			Likely benign (Feb 01, 2023)
6-160027283-C-T			Benign (Dec 31, 2019)
6-160027304-C-T		not specified	Uncertain significance (May 24, 2023)
6-160029591-A-G		not specified	Uncertain significance (Jul 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGF2R	protein_coding	protein_coding	ENST00000356956	48	144409

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	8.50e-8	125717	0	31	125748	0.000123

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.07	1203	1.42e+3	0.846	0.0000835	16329
Missense in Polyphen		347	503.96	0.68855		5625
Synonymous	-1.33	647	605	1.07	0.0000432	4796
Loss of Function	8.71	17	120	0.142	0.00000592	1464

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000232	0.000232
Ashkenazi Jewish	0.00	0.00
East Asian	0.000163	0.000163
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.000163	0.000163
South Asian	0.0000980	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transport of phosphorylated lysosomal enzymes from the Golgi complex and the cell surface to lysosomes. Lysosomal enzymes bearing phosphomannosyl residues bind specifically to mannose-6- phosphate receptors in the Golgi apparatus and the resulting receptor-ligand complex is transported to an acidic prelyosomal compartment where the low pH mediates the dissociation of the complex. This receptor also binds IGF2. Acts as a positive regulator of T-cell coactivation, by binding DPP4. {ECO:0000269|PubMed:10900005}.
• Pathway: Endocytosis - Homo sapiens (human);Lysosome - Homo sapiens (human);IGF-Ncore;miR-targeted genes in adipocytes - TarBase;miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;Neutrophil degranulation;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking;Innate Immune System;Immune System;Clathrin-mediated endocytosis;Cargo recognition for clathrin-mediated endocytosis;Retrograde transport at the Trans-Golgi-Network;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.705

Intolerance Scores

• loftool: 0.339
• rvis_EVS: -1.93
• rvis_percentile_EVS: 1.9

Haploinsufficiency Scores

• pHI: 0.145
• hipred: Y
• hipred_score: 0.747
• ghis: 0.448

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.977

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igf2r
• Phenotype: limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; renal/urinary system phenotype; embryo phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; normal phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; endocrine/exocrine gland phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: liver development;post-Golgi vesicle-mediated transport;receptor-mediated endocytosis;lysosomal transport;signal transduction;G protein-coupled receptor signaling pathway;spermatogenesis;post-embryonic development;animal organ regeneration;response to retinoic acid;positive regulation of apoptotic process;neutrophil degranulation;insulin-like growth factor receptor signaling pathway;membrane organization
• Cellular component: nuclear envelope lumen;lysosomal membrane;endosome;early endosome;late endosome;Golgi apparatus;trans-Golgi network;plasma membrane;integral component of plasma membrane;focal adhesion;cell surface;membrane;clathrin coat;transport vesicle;clathrin-coated vesicle;endocytic vesicle;trans-Golgi network transport vesicle;clathrin-coated vesicle membrane;secretory granule membrane;trans-Golgi network membrane;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: G-protein alpha-subunit binding;retinoic acid binding;insulin-like growth factor-activated receptor activity;protein binding;insulin-like growth factor binding;mannose binding;enzyme binding;insulin-like growth factor II binding;kringle domain binding;signaling receptor activity;identical protein binding;phosphoprotein binding