INS-IGF2

INS-IGF2 readthrough

Basic information

Region (hg38): 11:2132538-2161209

Links

ENSG00000129965 ∙ NCBI:723961 ∙ ∙ HGNC:33527 ∙ Uniprot:F8WCM5 ∙ 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 INS-IGF2 gene.

• Maturity-onset diabetes of the young type 10 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the INS-IGF2 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	7		8
missense	1	9	21	1		32
nonsense		1				1
start loss		1	1			2
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding		5	23	19	8	55
Total	1	17	46	27	8

Variants in INS-IGF2

This is a list of pathogenic ClinVar variants found in the INS-IGF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-2133009-T-G		IGF2-related disorder	Uncertain significance (Feb 26, 2024)
11-2133009-T-TG		Colorectal cancer	Pathogenic (-)
11-2133011-T-TG			Uncertain significance (Nov 28, 2023)
11-2133012-G-A		Inborn genetic diseases	Uncertain significance (Dec 16, 2022)
11-2133013-G-A			Uncertain significance (Nov 03, 2022)
11-2133017-G-T		not specified	Likely benign (Jan 23, 2024)
11-2133020-GC-G		not specified	Uncertain significance (Feb 19, 2024)
11-2133025-C-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Nov 18, 2023)
11-2133025-C-G		Inborn genetic diseases	Uncertain significance (Dec 19, 2021)
11-2133026-G-A			Likely benign (Sep 10, 2023)
11-2133027-T-G		Inborn genetic diseases	Uncertain significance (Jun 30, 2021)
11-2133031-C-A		Inborn genetic diseases	Uncertain significance (Jul 27, 2023)
11-2133034-G-T		IGF2-related disorder	Uncertain significance (Sep 16, 2024)
11-2133035-G-C		Inborn genetic diseases	Uncertain significance (Aug 20, 2023)
11-2133040-G-A			Likely pathogenic (Feb 01, 2021)
11-2133050-A-G		IGF2-related disorder	Likely benign (Oct 13, 2023)
11-2133057-AG-A			Uncertain significance (Jul 25, 2023)
11-2133063-C-T			Benign (Jan 28, 2024)
11-2133064-G-A		Inborn genetic diseases	Uncertain significance (Jan 07, 2022)
11-2133070-G-A			Uncertain significance (Jan 27, 2024)
11-2133086-C-T			Likely benign (Mar 02, 2022)
11-2133089-C-T			Benign (Aug 30, 2023)
11-2133091-C-G			Uncertain significance (Apr 14, 2023)
11-2133091-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Jan 08, 2024)
11-2133092-G-A			Likely benign (Oct 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
INS-IGF2	protein_coding	protein_coding	ENST00000397270	3	28672

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0558	0.873	125516	0	4	125520	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0114	91	91.3	0.997	0.00000569	1230
Missense in Polyphen		25	24.773	1.0092		295
Synonymous	-0.724	49	43.0	1.14	0.00000279	457
Loss of Function	1.51	3	7.43	0.404	4.36e-7	78

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	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: AMP-activated Protein Kinase (AMPK) Signaling;Type II diabetes mellitus (Consensus)

Intolerance Scores

• loftool: 0.314
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.12

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.386

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of signaling receptor activity
• Cellular component: extracellular region
• Molecular function: hormone activity