IGFLR1

IGF like family receptor 1

Basic information

Region (hg38): 19:35738801-35742453

Previous symbols: [ "U2AF1L4", "TMEM149" ]

Links

ENSG00000126246 ∙ NCBI:79713 ∙ OMIM:614143 ∙ HGNC:23620 ∙ Uniprot:Q9H665 ∙ 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 IGFLR1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGFLR1 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			36	3		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	36	3	0

Variants in IGFLR1

This is a list of pathogenic ClinVar variants found in the IGFLR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-35739294-C-A		not specified	Uncertain significance (Dec 10, 2024)
19-35739300-A-G		not specified	Uncertain significance (Dec 10, 2024)
19-35739308-A-G		not specified	Uncertain significance (Oct 31, 2023)
19-35739323-C-T		not specified	Likely benign (May 27, 2022)
19-35739339-G-A		not specified	Uncertain significance (May 06, 2024)
19-35739347-T-C		not specified	Uncertain significance (Feb 28, 2025)
19-35739351-C-T		not specified	Uncertain significance (Sep 26, 2023)
19-35739365-A-G		not specified	Uncertain significance (Nov 06, 2023)
19-35739404-A-G		not specified	Uncertain significance (Mar 02, 2023)
19-35739413-A-G		not specified	Uncertain significance (Feb 18, 2025)
19-35739425-G-A		not specified	Uncertain significance (Mar 05, 2025)
19-35739450-A-G		not specified	Uncertain significance (Aug 02, 2021)
19-35739492-C-T		not specified	Uncertain significance (Feb 12, 2025)
19-35739500-C-T		not specified	Uncertain significance (Nov 09, 2024)
19-35739543-G-C		not specified	Uncertain significance (Oct 27, 2022)
19-35739555-C-A		not specified	Uncertain significance (Feb 20, 2025)
19-35739564-C-T		not specified	Uncertain significance (Feb 23, 2023)
19-35739579-G-T		not specified	Uncertain significance (Sep 30, 2024)
19-35739593-C-T		not specified	Uncertain significance (Jun 17, 2022)
19-35739594-G-A		not specified	Uncertain significance (Sep 01, 2024)
19-35739712-C-T		not specified	Uncertain significance (Jan 17, 2025)
19-35739772-G-A		not specified	Uncertain significance (Mar 03, 2025)
19-35739775-G-A		not specified	Uncertain significance (Jan 04, 2025)
19-35739825-C-G		not specified	Uncertain significance (Aug 12, 2021)
19-35739872-G-T		not specified	Uncertain significance (Dec 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGFLR1	protein_coding	protein_coding	ENST00000592537	4	3297

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000259	0.523	125364	0	372	125736	0.00148

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.805	239	206	1.16	0.0000111	2188
Missense in Polyphen		91	62.452	1.4571		696
Synonymous	-1.22	115	99.5	1.16	0.00000568	820
Loss of Function	0.766	10	13.0	0.770	6.34e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00390	0.00389
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.00273	0.00272
Finnish	0.00	0.00
European (Non-Finnish)	0.00187	0.00186
Middle Eastern	0.00273	0.00272
South Asian	0.000819	0.000817
Other	0.000655	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable cell membrane receptor for the IGF-like family proteins. Binds IGFL1 and IGFL3 with a higher affinity. May also bind IGFL2. {ECO:0000269|PubMed:21454693}.

Recessive Scores

• pRec: 0.0911

Intolerance Scores

• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.85

Haploinsufficiency Scores

• pHI: 0.0884
• hipred: N
• hipred_score: 0.146
• ghis: 0.483

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• 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

Mouse Genome Informatics

• Gene name: Igflr1

Gene ontology

• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding