IGFL2

IGF like family member 2, the group of IGF like family

Basic information

Region (hg38): 19:46143106-46161298

Links

ENSG00000204866 ∙ NCBI:147920 ∙ OMIM:610545 ∙ HGNC:32929 ∙ Uniprot:Q6UWQ7 ∙ 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 IGFL2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGFL2 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			8	2		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	8	2	0

Variants in IGFL2

This is a list of pathogenic ClinVar variants found in the IGFL2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-46160450-T-A		not specified	Uncertain significance (Jul 14, 2023)
19-46160456-A-G		not specified	Uncertain significance (Jan 26, 2025)
19-46160620-C-T		not specified	Likely benign (Apr 26, 2023)
19-46160623-G-A		not specified	Likely benign (May 01, 2024)
19-46160701-A-G		not specified	Uncertain significance (Apr 15, 2024)
19-46160706-G-A		not specified	Uncertain significance (Jun 21, 2023)
19-46160731-G-A		not specified	Uncertain significance (Feb 12, 2025)
19-46160763-T-C		not specified	Uncertain significance (Apr 13, 2022)
19-46160806-A-G		not specified	Uncertain significance (Aug 13, 2021)
19-46161071-A-G		not specified	Uncertain significance (Feb 22, 2025)
19-46161077-C-T		not specified	Uncertain significance (Sep 10, 2024)
19-46161078-G-A		not specified	Uncertain significance (Sep 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGFL2	protein_coding	protein_coding	ENST00000434646	4	18194

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000777	0.553	125434	0	31	125465	0.000124

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.183	76	71.6	1.06	0.00000395	833
Missense in Polyphen		20	22.945	0.87164		297
Synonymous	0.497	26	29.4	0.883	0.00000179	246
Loss of Function	0.391	5	6.04	0.828	2.58e-7	74

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000534	0.000534
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000463	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.000327	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Potential ligand of the IGFLR1 cell membrane receptor. {ECO:0000269|PubMed:21454693}.

Intolerance Scores

• loftool: 0.781
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.189
• hipred: N
• hipred_score: 0.112
• ghis: 0.577

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0676

Gene Damage Prediction

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

Gene ontology

• Biological process: biological_process
• Cellular component: extracellular space
• Molecular function: signaling receptor binding