TNNI3K

protein-coding

TNNI3 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

NM_015978.3

Inheritance

AD

ClinVar variants

P:8U:832B:227

Top phenotype

Cardiac conduction disease with or without dilated cardiomyopathy

gnomAD constraint

pLI —, LoF o/e 1.16

Max pathogenic AF

—

Genomic locus

chr1:74,235,387-74,544,428

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~309.0 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

atrial conduction diseaseMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0014500

Submitter: Ambry Genetics

atrial conduction diseaseSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014500

Submitter: Genomics England PanelApp

dilated cardiomyopathyMODERATE

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).

atrial conduction diseaseSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0014500

Submitter: Labcorp Genetics (formerly Invitae)

cardiac conduction disease with or without dilated cardiomyopathy 1STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700388

Submitter: PanelApp Australia

atrial conduction diseaseSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0014500

Submitter: Orphanet

familial dilated cardiomyopathyLIMITED

Inheritance Pattern: AD

Disease ID:MONDO:0016333

Submitter: G2P

Clinical Genomic Database (CGD)

Cardiac conduction disease with or without dilated cardiomyopathyAD

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)

Refs: 24925317; 25791106; 30010057Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TNNI3K variants in ClinVar

15 Conditions Cataloged
not providedTotal: 1300
not specifiedTotal: 127
Inborn genetic diseasesTotal: 124
Atrial conduction diseaseTotal: 73
TNNI3K-related disorderTotal: 38
Cardiovascular phenotypeTotal: 25
Meniere diseaseTotal: 5
Primary dilated cardiomyopathyTotal: 4

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.

EffectPLPVUSLBBSum
synonymous
16
clinvar
178
clinvar
3
clinvar
197
missense
6
clinvar
690
clinvar
41
clinvar
2
clinvar
739
nonsense
2
clinvar
40
clinvar
1
clinvar
1
clinvar
44
start loss
2
clinvar
2
frameshift
41
clinvar
1
clinvar
42
splice donor/acceptor (+/-2bp)
43
clinvar
43
Total0883222161067

Highest pathogenic variant AF is 0.000007728652

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 20 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_015978.3RefSeqNP_057062.125MANE Select
ENST00000326637.8EnsemblENSP00000322251.325MANE Select
ENST00000525480.2EnsemblENSP00000433550.14Standard
ENST00000526236.5EnsemblENSP00000431465.15Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.5535324971.070.00002516093
Missense (PolyPhen)217219.020.990782661
Synonymous0.06281781790.9940.000008961769
Loss of Function-1.156757.61.160.00000299694

Population LoF Frequency

PopulationCAFp-valueStatus
African0.00290.0029notable
Latino/Admixed American0.00760.0074notable
Ashkenazi Jewish0.000100.000099rare
East Asian0.00240.0023notable
Finnish0.0000470.000046rare
European (Non-Finnish)0.00170.0017notable
South Asian0.00490.0047notable
Other0.00300.0028notable

dbNSFP Gene Annotations

Source: dbNSFP

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
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