CNTF

ciliary neurotrophic factor, the group of Interleukin 6 type cytokine family

Basic information

Region (hg38): 11:58622665-58625733

Links

ENSG00000242689 ∙ NCBI:1270 ∙ OMIM:118945 ∙ HGNC:2169 ∙ Uniprot:P26441 ∙ 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 CNTF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNTF 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			18	1	1	20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	18	1	1

Variants in CNTF

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

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

Position	Type	Phenotype	Significance	ClinVar
11-58622790-G-A		not specified	Uncertain significance (Oct 25, 2023)
11-58622808-G-A		not specified	Uncertain significance (May 06, 2022)
11-58622808-G-T		not specified	Uncertain significance (Mar 24, 2023)
11-58622810-T-C		not specified	Uncertain significance (Jan 26, 2022)
11-58622835-G-A		not specified	Uncertain significance (Jun 17, 2022)
11-58624028-G-A		CILIARY NEUROTROPHIC FACTOR POLYMORPHISM	Benign (-)
11-58624065-A-G			Benign (Dec 31, 2019)
11-58624067-C-A		not specified	Uncertain significance (Dec 20, 2023)
11-58624079-G-T		not specified	Uncertain significance (May 01, 2024)
11-58624185-G-C		not specified	Uncertain significance (Jul 08, 2022)
11-58624205-G-C		not specified	Uncertain significance (Feb 23, 2023)
11-58624283-C-G		not specified	Uncertain significance (Oct 03, 2023)
11-58624326-G-A		not specified	Uncertain significance (Feb 16, 2023)
11-58624349-A-T		not specified	Likely benign (Mar 20, 2024)
11-58624381-G-C		not specified	Uncertain significance (Aug 14, 2023)
11-58624407-A-G		not specified	Uncertain significance (Nov 21, 2023)
11-58624413-T-G		not specified	Uncertain significance (Feb 16, 2023)
11-58624449-G-A		not specified	Uncertain significance (Mar 29, 2023)
11-58624467-A-C		not specified	Uncertain significance (May 06, 2024)
11-58624476-T-G		not specified	Uncertain significance (Aug 08, 2023)
11-58624479-C-T		not specified	Uncertain significance (Aug 17, 2022)
11-58624484-C-T			Likely benign (Mar 01, 2023)
11-58624487-G-A		not specified	Uncertain significance (Mar 16, 2022)
11-58624499-A-G		not specified	Uncertain significance (Nov 23, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNTF	protein_coding	protein_coding	ENST00000361987	2	3053

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000234	0.311	125684	1	28	125713	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.653	139	119	1.17	0.00000694	1312
Missense in Polyphen		50	43.452	1.1507		524
Synonymous	-0.168	45	43.6	1.03	0.00000230	401
Loss of Function	0.00877	7	7.03	0.996	3.84e-7	73

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000870	0.0000870
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000108	0.000106
Middle Eastern	0.0000544	0.0000544
South Asian	0.000425	0.000392
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: CNTF is a survival factor for various neuronal cell types. Seems to prevent the degeneration of motor axons after axotomy.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Differentiation Pathway;Signaling by Interleukins;IL-6-type cytokine receptor ligand interactions;Cytokine Signaling in Immune system;Immune System;Interleukin-6 family signaling (Consensus)

Recessive Scores

• pRec: 0.281

Intolerance Scores

• loftool: 0.791
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.96

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.263

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.914

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cntf
• Phenotype: muscle phenotype; homeostasis/metabolism phenotype; immune system phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system 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)

Gene ontology

• Biological process: signal transduction;positive regulation of cell population proliferation;regulation of signaling receptor activity;positive regulation of gene expression;cytokine-mediated signaling pathway;positive regulation of tyrosine phosphorylation of STAT protein;negative regulation of neuron apoptotic process;negative regulation of photoreceptor cell differentiation;regulation of retinal cell programmed cell death;astrocyte activation;muscle organ morphogenesis;neuron development;positive regulation of axon regeneration;ciliary neurotrophic factor-mediated signaling pathway
• Cellular component: extracellular region;extracellular space;cytoplasm;axon
• Molecular function: cytokine activity;ciliary neurotrophic factor receptor binding;interleukin-6 receptor binding;protein binding;growth factor activity;protein-containing complex binding