LIF
LIF interleukin 6 family cytokine, the group of Interleukin 6 type cytokine family|Receptor ligands
Basic information
Region (hg38): 22:30240453-30246759
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the LIF 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 | 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 LIF
This is a list of pathogenic ClinVar variants found in the LIF region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 22-30243664-G-A | not specified | Uncertain significance (Dec 02, 2022) | ||
| 22-30243785-A-G | not specified | Uncertain significance (Nov 21, 2022) | ||
| 22-30243809-C-A | not specified | Uncertain significance (Apr 23, 2024) | ||
| 22-30243839-C-T | not specified | Uncertain significance (Jun 09, 2022) | ||
| 22-30243851-G-A | not specified | Uncertain significance (Nov 06, 2023) | ||
| 22-30243962-C-G | not specified | Uncertain significance (Jan 17, 2024) | ||
| 22-30244000-G-A | not specified | Uncertain significance (Mar 11, 2024) | ||
| 22-30244004-C-T | not specified | Benign/Likely benign (Nov 01, 2022) | ||
| 22-30244034-T-C | not specified | Uncertain significance (Nov 21, 2022) | ||
| 22-30244844-G-A | not specified | Uncertain significance (Nov 29, 2023) | ||
| 22-30244868-G-A | not specified | Uncertain significance (Mar 02, 2023) | ||
| 22-30244880-G-A | not specified | Uncertain significance (Jun 16, 2023) | ||
| 22-30246688-A-T | not specified | Uncertain significance (Dec 16, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| LIF | protein_coding | protein_coding | ENST00000249075 | 3 | 6405 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.524 | 0.461 | 125721 | 0 | 4 | 125725 | 0.0000159 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.398 | 109 | 121 | 0.898 | 0.00000776 | 1315 |
| Missense in Polyphen | 35 | 47.037 | 0.7441 | 568 | ||
| Synonymous | -0.694 | 66 | 59.2 | 1.11 | 0.00000446 | 424 |
| Loss of Function | 1.96 | 1 | 6.30 | 0.159 | 3.55e-7 | 68 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000569 | 0.0000462 |
| European (Non-Finnish) | 0.00000880 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: LIF has the capacity to induce terminal differentiation in leukemic cells. Its activities include the induction of hematopoietic differentiation in normal and myeloid leukemia cells, the induction of neuronal cell differentiation, and the stimulation of acute-phase protein synthesis in hepatocytes.;
- Pathway
- Jak-STAT signaling pathway - Homo sapiens (human);TNF signaling pathway - Homo sapiens (human);Signaling pathways regulating pluripotency of stem cells - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;MicroRNAs in cardiomyocyte hypertrophy;Adipogenesis;ESC Pluripotency Pathways;Interleukin-10 signaling;Interleukin-4 and 13 signaling;TGF-beta Receptor Signaling;Signaling by Interleukins;IL-6-type cytokine receptor ligand interactions;nfat and hypertrophy of the heart ;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;GPCR signaling-G alpha q;GPCR signaling-cholera toxin;GPCR signaling-pertussis toxin;Immune System;GPCR signaling-G alpha s Epac and ERK;GPCR signaling-G alpha s PKA and ERK;JAK STAT pathway and regulation;LIF signaling;Direct p53 effectors;GPCR signaling-G alpha i;Validated transcriptional targets of AP1 family members Fra1 and Fra2;Interleukin-6 family signaling
(Consensus)
Recessive Scores
- pRec
- 0.783
Intolerance Scores
- loftool
- 0.397
- rvis_EVS
- 0.28
- rvis_percentile_EVS
- 71.27
Haploinsufficiency Scores
- pHI
- 0.249
- hipred
- Y
- hipred_score
- 0.611
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Lif
- Phenotype
- reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; liver/biliary system phenotype; respiratory system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); embryo phenotype; skeleton phenotype; immune system phenotype; vision/eye phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); digestive/alimentary phenotype; muscle phenotype; endocrine/exocrine gland phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- blood vessel remodeling;immune response;tyrosine phosphorylation of STAT protein;multicellular organism development;embryo implantation;positive regulation of cell population proliferation;negative regulation of cell population proliferation;regulation of signaling receptor activity;cytokine-mediated signaling pathway;stem cell population maintenance;positive regulation of peptidyl-serine phosphorylation;positive regulation of peptidyl-serine phosphorylation of STAT protein;positive regulation of tyrosine phosphorylation of STAT protein;positive regulation of MAPK cascade;regulation of cell differentiation;positive regulation of macrophage differentiation;negative regulation of meiotic nuclear division;positive regulation of transcription by RNA polymerase II;decidualization;negative regulation of hormone secretion;lung alveolus development;muscle organ morphogenesis;neuron development;positive regulation of astrocyte differentiation;leukemia inhibitory factor signaling pathway;stem cell differentiation;positive regulation of peptidyl-tyrosine phosphorylation;lung vasculature development;lung lobe morphogenesis;trophoblast giant cell differentiation;spongiotrophoblast differentiation;negative regulation of ERK1 and ERK2 cascade;positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis;regulation of metanephric nephron tubule epithelial cell differentiation;positive regulation of protein localization to nucleus;positive regulation of histone H3-K27 acetylation;regulation of RNA polymerase II regulatory region sequence-specific DNA binding
- Cellular component
- extracellular region;extracellular space;cytosol
- Molecular function
- signaling receptor binding;cytokine activity;leukemia inhibitory factor receptor binding;protein binding;growth factor activity