IGFBPL1

insulin like growth factor binding protein like 1, the group of I-set domain containing

Basic information

Region (hg38): 9:38406528-38424454

Links

ENSG00000137142 ∙ NCBI:347252 ∙ OMIM:610413 ∙ HGNC:20081 ∙ Uniprot:Q8WX77 ∙ 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 IGFBPL1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IGFBPL1 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				2		2
missense			44			44
nonsense						0
start loss						0
frameshift					2	2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	2	2

Variants in IGFBPL1

This is a list of pathogenic ClinVar variants found in the IGFBPL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-38411405-T-C		not specified	Uncertain significance (Nov 13, 2024)
9-38411406-GCGGTCAT-G			Benign (Dec 31, 2019)
9-38411407-C-T		not specified	Uncertain significance (Jan 24, 2023)
9-38411418-A-AT			Benign (Dec 31, 2019)
9-38411451-A-C		not specified	Uncertain significance (Jul 14, 2021)
9-38411461-G-A		not specified	Uncertain significance (Jan 03, 2025)
9-38411476-G-A		not specified	Uncertain significance (Apr 19, 2024)
9-38411478-C-G		not specified	Uncertain significance (Aug 28, 2024)
9-38411495-T-C		not specified	Uncertain significance (Dec 23, 2024)
9-38411506-T-C		not specified	Uncertain significance (Dec 15, 2023)
9-38411536-C-T		not specified	Uncertain significance (Dec 22, 2023)
9-38411544-G-T		not specified	Uncertain significance (Jul 20, 2021)
9-38413242-T-C		not specified	Uncertain significance (Mar 11, 2025)
9-38413277-C-T		not specified	Uncertain significance (Jul 09, 2021)
9-38413289-G-C		not specified	Uncertain significance (Jan 29, 2024)
9-38413291-T-C		not specified	Uncertain significance (Sep 03, 2024)
9-38413293-T-A		not specified	Uncertain significance (May 17, 2023)
9-38413334-C-A		not specified	Uncertain significance (Mar 06, 2025)
9-38414141-A-T		not specified	Uncertain significance (Nov 22, 2021)
9-38414167-T-C		not specified	Uncertain significance (Jan 24, 2023)
9-38414179-C-T		not specified	Uncertain significance (Dec 08, 2023)
9-38414201-G-C		not specified	Uncertain significance (Oct 07, 2024)
9-38423976-G-A		not specified	Uncertain significance (Feb 26, 2024)
9-38423981-G-A			Likely benign (May 01, 2022)
9-38424009-T-A		not specified	Uncertain significance (Feb 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IGFBPL1	protein_coding	protein_coding	ENST00000377694	4	15454

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000404	0.404	125477	3	268	125748	0.00108

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.438	87	99.3	0.876	0.00000545	1705
Missense in Polyphen		31	38.272	0.81		686
Synonymous	0.761	37	43.4	0.853	0.00000263	623
Loss of Function	0.260	7	7.78	0.899	5.01e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0137	0.0132
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.00	0.00
South Asian	0.0000655	0.0000653
Other	0.00115	0.00114

dbNSFP

Source: dbNSFP

• Function: FUNCTION: IGF-binding proteins prolong the half-life of IGFs and have been shown to either inhibit or stimulate the growth promoting effects of the IGFs in cell culture. They alter the interaction of IGFs with their cell surface receptors (By similarity). May be a putative tumor suppressor protein. {ECO:0000250, ECO:0000269|PubMed:15845387}.

Haploinsufficiency Scores

• pHI: 0.183
• hipred: N
• hipred_score: 0.146
• ghis: 0.478

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.199

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Igfbpl1

Gene ontology

• Biological process: regulation of cell growth;cellular response to tumor cell
• Cellular component: extracellular space
• Molecular function: molecular_function;insulin-like growth factor binding