CNTFR

ciliary neurotrophic factor receptor, the group of Fibronectin type III domain containing|Immunoglobulin like domain containing

Basic information

Region (hg38): 9:34551431-34590140

Links

ENSG00000122756 ∙ NCBI:1271 ∙ OMIM:118946 ∙ HGNC:2170 ∙ Uniprot:P26992 ∙ 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 CNTFR gene.

• Inborn genetic diseases (9 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CNTFR 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in CNTFR

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

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

Position	Type	Phenotype	Significance	ClinVar
9-34552219-C-T		not specified	Uncertain significance (Jan 26, 2023)
9-34552686-C-A		not specified	Uncertain significance (Aug 10, 2021)
9-34552734-C-T		not specified	Uncertain significance (Jul 26, 2023)
9-34552839-C-T		not specified	Uncertain significance (Feb 16, 2023)
9-34556323-C-G		Malignant tumor of prostate	Uncertain significance (-)
9-34557625-T-A		not specified	Uncertain significance (Jul 14, 2021)
9-34557885-G-A		not specified	Uncertain significance (Dec 21, 2022)
9-34564626-G-A		not specified	Uncertain significance (Sep 26, 2023)
9-34564630-G-T		not specified	Uncertain significance (Nov 15, 2021)
9-34564707-C-T		not specified	Uncertain significance (Sep 21, 2023)
9-34564715-A-G		not specified	Uncertain significance (Dec 05, 2022)
9-34564745-C-T		not specified	Uncertain significance (Mar 06, 2023)
9-34564794-C-T		not specified	Uncertain significance (Nov 17, 2023)
9-34564826-G-A		not specified	Uncertain significance (Jun 07, 2023)
9-34568918-C-T		not specified	Likely benign (Jan 17, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CNTFR	protein_coding	protein_coding	ENST00000378980	7	38692

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.955	0.0445	125742	0	5	125747	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.60	166	235	0.706	0.0000146	2366
Missense in Polyphen		38	60.339	0.62977		571
Synonymous	0.442	98	104	0.945	0.00000759	777
Loss of Function	3.56	2	18.6	0.108	9.65e-7	182

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000469	0.0000462
European (Non-Finnish)	0.0000354	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to CNTF. The alpha subunit provides the receptor specificity.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);JAK-STAT-Core;Adipogenesis;Signaling by Interleukins;IL-6-type cytokine receptor ligand interactions;Cytokine Signaling in Immune system;JAK STAT MolecularVariation 1;Immune System;JAK STAT MolecularVariation 2;JAK STAT pathway and regulation;Interleukin-6 family signaling (Consensus)

Recessive Scores

• pRec: 0.345

Intolerance Scores

• loftool: 0.110
• rvis_EVS: -0.82
• rvis_percentile_EVS: 11.68

Haploinsufficiency Scores

• pHI: 0.445
• hipred: Y
• hipred_score: 0.853
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.895

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cntfr
• 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: suckling behavior;brainstem development;signal transduction;nervous system development;sex differentiation;positive regulation of cell population proliferation;cytokine-mediated signaling pathway;negative regulation of neuron apoptotic process;skeletal muscle organ development;ciliary neurotrophic factor-mediated signaling pathway
• Cellular component: plasma membrane;external side of plasma membrane;apical plasma membrane;extrinsic component of membrane;anchored component of membrane;receptor complex;ciliary neurotrophic factor receptor complex;CNTFR-CLCF1 complex
• Molecular function: cytokine receptor activity;ciliary neurotrophic factor receptor activity;signaling receptor binding;protein binding;cytokine binding;interleukin-27 receptor binding