CTF1

cardiotrophin 1, the group of Interleukin 6 type cytokine family

Basic information

Region (hg38): 16:30896613-30903547

Links

ENSG00000150281 ∙ NCBI:1489 ∙ OMIM:600435 ∙ HGNC:2499 ∙ Uniprot:Q16619 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• dilated cardiomyopathy (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CTF1 gene.

• Dilated Cardiomyopathy, Dominant (136 variants)
• not specified (23 variants)
• Cardiomyopathy (13 variants)
• Inborn genetic diseases (8 variants)
• not provided (6 variants)
• Hypertrophic cardiomyopathy (2 variants)
• Primary familial hypertrophic cardiomyopathy (1 variants)
• Primary dilated cardiomyopathy (1 variants)
• Dilated Cardiomyopathy, Dominant;not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTF1 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			3	37	1	41
missense			65	5		70
nonsense			3			3
start loss						0
frameshift			5			5
inframe indel			9			9
splice donor/acceptor (+/-2bp)			1			1
splice region			1	1		2
non coding			5	7	2	14
Total	0	0	91	49	3

Variants in CTF1

This is a list of pathogenic ClinVar variants found in the CTF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-30896674-G-C		not specified	Uncertain significance (Mar 08, 2011)
16-30896677-C-CT		Cardiomyopathy	Likely benign (Jun 02, 2021)
16-30898385-C-G		Dilated Cardiomyopathy, Dominant	Benign (Jan 22, 2024)
16-30899398-C-G		Dilated Cardiomyopathy, Dominant	Likely benign (May 17, 2023)
16-30899398-C-T		Dilated Cardiomyopathy, Dominant	Likely benign (Nov 02, 2023)
16-30899400-C-T		Dilated Cardiomyopathy, Dominant	Likely benign (Apr 24, 2023)
16-30899402-C-A		Dilated Cardiomyopathy, Dominant	Likely benign (Sep 10, 2023)
16-30899402-C-G		Dilated Cardiomyopathy, Dominant	Uncertain significance (Mar 03, 2023)
16-30899402-C-T		Dilated Cardiomyopathy, Dominant	Likely benign (Sep 12, 2023)
16-30899403-C-G		not specified • Cardiomyopathy	Conflicting classifications of pathogenicity (Jan 10, 2019)
16-30899414-G-A		Dilated Cardiomyopathy, Dominant	Uncertain significance (Aug 12, 2021)
16-30899415-A-C		Dilated Cardiomyopathy, Dominant	Uncertain significance (Dec 24, 2021)
16-30899421-C-G		Dilated Cardiomyopathy, Dominant	Uncertain significance (Jul 05, 2022)
16-30899423-C-T		Dilated Cardiomyopathy, Dominant • not specified	Uncertain significance (Oct 27, 2022)
16-30899426-A-G		Dilated Cardiomyopathy, Dominant	Uncertain significance (Jul 26, 2021)
16-30899444-C-A		not specified • Dilated Cardiomyopathy, Dominant	Likely benign (Dec 07, 2023)
16-30899453-C-G		Dilated Cardiomyopathy, Dominant	Uncertain significance (Oct 04, 2023)
16-30899464-C-A		Dilated Cardiomyopathy, Dominant	Likely benign (Apr 06, 2023)
16-30899472-G-A		Dilated Cardiomyopathy, Dominant • not specified	Conflicting classifications of pathogenicity (Sep 06, 2023)
16-30899474-CAGA-C		Dilated Cardiomyopathy, Dominant	Uncertain significance (Aug 05, 2021)
16-30899480-C-T		Dilated Cardiomyopathy, Dominant	Uncertain significance (Sep 23, 2022)
16-30899490-C-T		Dilated Cardiomyopathy, Dominant • not specified	Uncertain significance (Feb 28, 2023)
16-30899491-G-A		not specified	Likely benign (Jan 02, 2014)
16-30899492-C-A		Dilated Cardiomyopathy, Dominant	Uncertain significance (Sep 10, 2022)
16-30899500-C-T		Dilated Cardiomyopathy, Dominant	Likely benign (Aug 16, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CTF1	protein_coding	protein_coding	ENST00000279804	3	6954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0419	0.674	125590	0	7	125597	0.0000279

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.811	29	44.2	0.657	0.00000229	1197
Missense in Polyphen		15	17.407	0.86173		364
Synonymous	0.218	18	19.2	0.937	9.66e-7	485
Loss of Function	0.509	2	2.94	0.680	1.24e-7	58

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000615	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000265	0.0000264
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Induces cardiac myocyte hypertrophy in vitro. Binds to and activates the ILST/gp130 receptor.
• Pathway: Jak-STAT signaling pathway - Homo sapiens (human);Cytokine-cytokine receptor interaction - Homo sapiens (human);Physiological and Pathological Hypertrophy of the Heart;MicroRNAs in cardiomyocyte hypertrophy;Signaling by Interleukins;IL-6-type cytokine receptor ligand interactions;nfat and hypertrophy of the heart ;Cytokine Signaling in Immune system;Immune System;Interleukin-6 family signaling (Consensus)

Recessive Scores

• pRec: 0.366

Haploinsufficiency Scores

• pHI: 0.175
• hipred: N
• hipred_score: 0.396
• ghis: 0.618

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.841

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ctf1
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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: cell surface receptor signaling pathway;cell-cell signaling;nervous system development;muscle organ development;cell population proliferation;positive regulation of cell population proliferation;regulation of signaling receptor activity;cytokine-mediated signaling pathway;positive regulation of tyrosine phosphorylation of STAT protein;neuron development;leukemia inhibitory factor signaling pathway
• Cellular component: extracellular region;extracellular space
• Molecular function: cytokine activity;leukemia inhibitory factor receptor binding;protein binding