LIF

LIF interleukin 6 family cytokine, the group of Interleukin 6 type cytokine family|Receptor ligands

Basic information

Region (hg38): 22:30240453-30246759

Links

ENSG00000128342 ∙ NCBI:3976 ∙ OMIM:159540 ∙ HGNC:6596 ∙ Uniprot:P15018 ∙ 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 LIF gene.

• not_specified (31 variants)
• not_provided (1 variants)

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. These statistics are base on transcript: NM_000002309.5. 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						0
missense			29	2		31
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	29	2	0

GnomAD

Source: gnomAD

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
		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: dbNSFP

• 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

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

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