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.

• not_specified (65 variants)
• not_provided (4 variants)

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. These statistics are base on transcript: NM_001007563.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2		2
missense			65			65
nonsense						0
start loss						0
frameshift					2	2
splice donor/acceptor (+/-2bp)						0
Total	0	0	65	2	2

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