CTF1

protein-coding

cardiotrophin 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

NM_001330.5

Inheritance

AD

ClinVar variants

U:127B:70

Top phenotype

Cardiomyopathy

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr16:30,896,614-30,903,547

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~6.9 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

dilated cardiomyopathyLIMITED

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).

familial dilated cardiomyopathyLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0016333

Submitter: G2P

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CTF1 variants in ClinVar

6 Conditions Cataloged
not providedTotal: 204
not specifiedTotal: 53
CardiomyopathyTotal: 12
Primary dilated cardiomyopathyTotal: 2
Hypertrophic cardiomyopathyTotal: 2
Dilated Cardiomyopathy, DominantTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
60
clinvar
1
clinvar
62
missense
114
clinvar
9
clinvar
123
nonsense
4
clinvar
4
start loss
0
frameshift
7
clinvar
7
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total00127691197
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_001330.5RefSeqNP_001321.13MANE Select
ENST00000279804.3EnsemblENSP00000279804.23MANE Select
NM_001142544.3RefSeqNP_001136016.13Standard
ENST00000395019.3EnsemblENSP00000378465.33Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.8112944.20.6570.000002291197
Missense (PolyPhen)1517.4070.86173364
Synonymous0.2181819.20.9379.66e-7485
Loss of Function0.50922.940.6801.24e-758

Population LoF Frequency

PopulationCAFp-valueStatus
African0.0000620.000062rare
Latino/Admixed American00.0absent
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000270.000026rare
South Asian0.0000650.000065rare
Other0.000160.00016rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
For research and educational, non-commercial use only. Not for clinical or diagnostic use. GeneBe does not provide medical advice. Data use for AI modeling is prohibited: if used, the cost is $0.001 per byte of downloaded uncompressed data.