IGFL1

IGF like family member 1, the group of IGF like family

Basic information

Region (hg38): 19:46229741-46231243

Links

ENSG00000188293 ∙ NCBI:374918 ∙ OMIM:610544 ∙ HGNC:24093 ∙ Uniprot:Q6UW32 ∙ 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 IGFL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGFL1 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in IGFL1

This is a list of pathogenic ClinVar variants found in the IGFL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-46229785-G-A		not specified	Uncertain significance (Apr 10, 2023)
19-46230119-A-G		not specified	Uncertain significance (Mar 06, 2023)
19-46230312-C-T		not specified	Uncertain significance (Oct 10, 2023)
19-46230334-T-C		not specified	Uncertain significance (Nov 21, 2022)
19-46230341-C-G		not specified	Uncertain significance (Aug 12, 2021)
19-46230351-C-T		not specified	Uncertain significance (Sep 13, 2023)
19-46230372-G-A		not specified	Uncertain significance (Aug 13, 2021)
19-46230397-C-T		not specified	Uncertain significance (Apr 20, 2024)
19-46230434-G-T		not specified	Uncertain significance (Feb 13, 2024)
19-46230480-G-A		not specified	Likely benign (Dec 26, 2023)
19-46230489-C-T		not specified	Uncertain significance (Jul 11, 2022)
19-46230490-G-A		not specified	Uncertain significance (Apr 17, 2024)
19-46230503-C-G		not specified	Uncertain significance (Oct 27, 2023)
19-46230510-T-C		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGFL1	protein_coding	protein_coding	ENST00000437936	4	1492

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.99e-8	0.0396	124625	0	30	124655	0.000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0536	66	64.8	1.02	0.00000379	718
Missense in Polyphen		9	14.787	0.60866		191
Synonymous	0.815	21	26.3	0.798	0.00000179	198
Loss of Function	-1.11	10	6.87	1.46	3.80e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000862	0.000797
Ashkenazi Jewish	0.00	0.00
East Asian	0.000343	0.000334
Finnish	0.00	0.00
European (Non-Finnish)	0.0000266	0.0000265
Middle Eastern	0.000343	0.000334
South Asian	0.000196	0.000196
Other	0.000167	0.000165

dbNSFP

Source: dbNSFP

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

Recessive Scores

• pRec: 0.0936

Intolerance Scores

• loftool: 0.754
• rvis_EVS: 0.68
• rvis_percentile_EVS: 84.93

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: 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

• Cellular component: extracellular space
• Molecular function: signaling receptor binding;protein binding