CTF1
protein-codingcardiotrophin 1, the group of Interleukin 6 type cytokine family
Gene summary
The protein encoded by this gene is a secreted cytokine that induces cardiac myocyte hypertrophy in vitro. It has been shown to bind and activate the ILST/gp130 receoptor. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~6.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0005021
Submitter: ClinGen
CTF-1 was originally evaluated for DCM by the ClinGen DCM GCEP on February 28, 2020. Evidence of the association of this gene with DCM was re-evaluated using SOP v10 on June 14 2024. The overall genetic evidence points decreased at recuration. With these updates, the clinical validity classification did not change and remains Limited. A summary of the information contributing to the classification of this gene at the time of re-evaluation is summarized herein. CTF-1 was first reported in relation to autosomal dominant dilated cardiomyopathy in 2000 (Erdmann J et al, PMID: 11058912). Human genetic evidence supporting this gene-disease relationship includes case-level data. At least 7 variants (6 missense and 1 spice site variant) have been reported in humans. Variants in this gene have been reported in at least 10 probands in 3 publications (Erdmann et al, 2000, PMID: 11058912; Pugh et al, 2014, PMID: 24503780; Akinrinade et al, 2015, PMID: 26084686). No segregation data has been reported. This gene-disease relationship has been studied in at least one case-control study at the single variant level (Erdmann et al, 2000, PMID: 11058912), however, this variant was subsequently found to be more commonly expressed in the population than would be expected to explain disease. There is a lack of robust human genetic evidence demonstrating this gene-disease relationship in the literature. No new publications demonstrating CTF-1 variants in DCM were identified during re-curation. Evaluation of the previously identified variants found that all but one of the variants have subsequently been found at a frequency higher than would be expected for a monogenic, pathogenic effect in population reference data sets. This gene-disease association is supported by one animal model (rat) and expression studies (Pennica et al, 1995, PMID: 7862649; Pennica et al, 1996, PMID: 8833032; Zolk et al, 2002, PMID: 12234945; Lopez et al, 2014, PMID: 24366078; Robador et al, 2011, PMID: 21771897; Lopez-Andres et al, 2012, PMID: 22733458). Two additional human expression studies (Sharif et al, 2021, PMID: 34447655; Rubiś et al, 2021, PMID: 34071085) were identified during re-curation. In summary, no convincing evidence for a causal role for CTF-1 and autosomal dominant DCM has been reported. Although this gene-disease assertion is supported by one animal model (rat) and multiple expression studies (human) no reports have directly implicated the gene in humans. Additionally, there has been a lack of new supporting evidence in the four year period since the previous curation. In summary, there is limited evidence to support this gene-disease relationship. More evidence is needed to support the relationship of CTF-1 and AD DCM.This classification was approved by the ClinGen Dilated Cardiomyopathy Working Group on June 14 2024 (SOP Version 10).
Inheritance Pattern: AD
Disease ID:MONDO:0016333
Submitter: G2P
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CTF1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001330.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 60 | 1 | 62 | ||
| missense | 114 | 9 | 123 | |||
| nonsense | 4 | 4 | ||||
| start loss | 0 | |||||
| frameshift | 7 | 7 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 127 | 69 | 1 | 197 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001321.1 | 3 | MANE Select | |
| Ensembl | ENSP00000279804.2 | 3 | MANE Select | |
| RefSeq | NP_001136016.1 | 3 | Standard | |
| Ensembl | ENSP00000378465.3 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- 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
Biological Process
- cell surface receptor signaling pathway
- cell-cell signaling
- nervous system development
- muscle organ development
- cell population proliferation
Molecular Function
- cytokine activity
- leukemia inhibitory factor receptor binding
- protein binding
Cellular Component
- extracellular region
- extracellular space
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000279804
- Coding exons
- 3
- Length
- 6954
- Individuals with no LoFs
- 125590
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 7
- Defined
- 125597
- p
- 0.0000279
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.811 | 29 | 44.2 | 0.657 | 0.00000229 | 1197 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Induces cardiac myocyte hypertrophy in vitro. Binds to and activates the ILST/gp130 receptor.;
Recessive Scores
- pRec
- 0.366
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- H
- Indispensability pred.
- E
- Indispensability score
- 0.841
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |