TNNI3K
protein-codingTNNI3 interacting kinase, the group of Ankyrin repeat domain containing
Gene summary
This gene encodes a protein that belongs to the MAP kinase kinase kinase (MAPKKK) family of protein kinases. The protein contains ankyrin repeat, protein kinase and serine-rich domains and is thought to play a role in cardiac physiology. [provided by RefSeq, Sep 2012]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~309.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0014500
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0014500
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0005021
Submitter: ClinGen
TNNI3K was evaluated for autosomal dominant dilated cardiomyopathy (DCM). TNNI3K was originally evaluated for DCM by the ClinGen DCM GCEP on August 12, 2020. Evidence of the association of this gene with DCM was re-evaluated using SOP v11 on November 1, 2024. As a result, the association was increased from limited to moderate. A summary of the information contributing to the classification of this gene at the time of re-evaluation is summarized herein. Genetic data published supports an association with DCM presenting with or without cardiac conduction disease, including several studies of families showing TNNI3K variants segregating in individuals with conduction disease. Affected individuals may or may not also have DCM. Conduction disease may present years before cardiomyopathy. (PMID: 37199186; 30010057; 24925317). At least 4 missense variants have been reported in individuals with both cardiac conduction disease and DCM, one of which was reported in three families, the other in six. One intronic variant was reported in a family with conduction disease and DCM and was identified in one person with only DCM noted. This family was not scored, however, since the authors asserted a loss of function (LoF) mechanism, which does not appear to be a mechanism of disease at this time (PMID: 29355681). The mechanism of disease has not been established, though LoF is debated given the lack of experimental evidence and the presence of homozygous LoF variants in the general population. Gene-based burden testing found that rare missense variants in TNNI3K were significantly associated with DCM whereas LoF variants were not (PMID: 37199186). TNNI3K has cardiac-specific expression in the fetal and adult heart and interacts with cardiac troponin I (PMID: 12721663). Experimental evidence for this gene included model systems using transgenic mouse lines expressing WT human TNNI3K (PMID: 19763165). TNNI3K expression alone did not result in overt cardiomyopathy or decreased survival. Transgenic mice showed greater diastolic and systolic dysfunction and significantly reduced fractional shortening compared to the control mice after undergoing transthoracic aortic constriction (TAC). Double transgenic mice were created (Calsequestrin (Csq) and TNNI3K WT). In the CSQ mouse, cardiac-specific overexpression of the CSQ protein leads to DCM, recapitulating many of the hallmarks of human DCM. The double transgenic mice had profoundly premature death, significantly decreased fractional shortening, larger heart size and histological staining showing obvious chamber dilation, suggesting that TNNI3K modifies disease progression. TNNI3K overexpression increased heart weight, cardiomyocyte diameter, cardiac fibrosis and reduced fractional shortening in transgenic mice and TNNI3K phosphorylation was significantly induced by transverse aortic constriction (PMID: 23085512). In summary, there is moderate evidence to support this gene-disease relationship. More evidence is needed to establish the relationship of TNNI3K with autosomal dominant DCM definitively. This classification was approved by the ClinGen Dilated Cardiomyopathy Working Group on 11/1/2024 (SOP Version 10).
Inheritance Pattern: AD
Disease ID:MONDO:0014500
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0700388
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0014500
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0016333
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular
Intervention: Cardiovascular
Rationale: Individuals have been described with arrhythmia and cardiomyopathy, and awareness may allow early medical/surgical management (eg, medical management and catheter-based ablation of cardiac foci has been described as beneficial)
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TNNI3K variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_015978.3. 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 | 16 | 178 | 3 | 197 | ||
| missense | 6 | 690 | 41 | 2 | 739 | |
| nonsense | 2 | 40 | 1 | 1 | 44 | |
| start loss | 2 | 2 | ||||
| frameshift | 41 | 1 | 42 | |||
| splice donor/acceptor (+/-2bp) | 43 | 43 | ||||
| Total | 0 | 8 | 832 | 221 | 6 | 1067 |
Highest pathogenic variant AF is 0.000007728652
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_057062.1 | 25 | MANE Select | |
| Ensembl | ENSP00000322251.3 | 25 | MANE Select | |
| Ensembl | ENSP00000433550.1 | 4 | Standard | |
| Ensembl | ENSP00000431465.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- regulation of heart rate
- protein phosphorylation
- regulation of cardiac muscle contraction
- bundle of His cell to Purkinje myocyte communication
- regulation of cardiac conduction
Molecular Function
- protein kinase activity
- protein serine/threonine kinase activity
- protein binding
- ATP binding
- protein C-terminus binding
Cellular Component
- nucleus
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000370891
- Coding exons
- 27
- Length
- 346166
- Individuals with no LoFs
- 125048
- Homozygous LoFs
- 5
- Heterozygous LoFs
- 695
- Defined
- 125748
- p
- 0.00279
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.553 | 532 | 497 | 1.07 | 0.0000251 | 6093 |
| Missense (PolyPhen) | 217 | 219.02 | 0.99078 | 2661 | ||
| Synonymous | 0.0628 | 178 | 179 | 0.994 | 0.00000896 | 1769 |
| Loss of Function | -1.15 | 67 | 57.6 | 1.16 | 0.00000299 | 694 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0029 | 0.0029 | notable |
| Latino/Admixed American | 0.0076 | 0.0074 | notable |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.0024 | 0.0023 | notable |
| Finnish | 0.000047 | 0.000046 | rare |
| European (Non-Finnish) | 0.0017 | 0.0017 | notable |
| South Asian | 0.0049 | 0.0047 | notable |
| Other | 0.0030 | 0.0028 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May play a role in cardiac physiology. {ECO:0000303|PubMed:12721663}.;
- Disease
- DISEASE: Cardiac conduction disease with or without dilated cardiomyopathy (CCDD) [MIM:616117]: A cardiac disorder characterized by atrial tachyarrhythmia and conduction system disease. Some patients have dilated cardiomyopathy. {ECO:0000269|PubMed:24925317}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.108
Intolerance Scores
- LoFtool
- 0.547
- RVIS EVS
- -0.35
- RVIS percentile EVS
- 29.59
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.822