TNNI1
protein-codingtroponin I1, slow skeletal type, the group of Troponin complex subunits
Gene summary
Troponin proteins associate with tropomyosin and regulate the calcium sensitivity of the myofibril contractile apparatus of striated muscles. Troponin I (TnI), along with troponin T (TnT) and troponin C (TnC), is one of 3 subunits that form the troponin complex of the thin filaments of striated muscle. TnI is the inhibitory subunit; blocking actin-myosin interactions and thereby mediating striated muscle relaxation. The TnI subfamily contains three genes: TnI-skeletal-fast-twitch, TnI-skeletal-slow-twitch, and TnI-cardiac. The TnI-fast and TnI-slow genes are expressed in fast-twitch and slow-twitch skeletal muscle fibers, respectively, while the TnI-cardiac gene is expressed exclusively in cardiac muscle tissue. This gene encodes the Troponin-I-skeletal-slow-twitch protein. This gene is expressed in cardiac and skeletal muscle during early development but is restricted to slow-twitch skeletal muscle fibers in adults. The encoded protein prevents muscle contraction by inhibiting calcium-mediated conformational changes in actin-myosin complexes. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~26.1 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0008779
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0015738
Submitter: ClinGen
*TNNI1* was first reported in relation to autosomal recessive congenital myopathy in 2024 (Donkervoort *et al.* PMID: 38569017). Per criteria outlined by the ClinGen Lumping and Splitting guidelines, we found differences in inheritance pattern, molecular mechanism, and phenotypic variability for *TNNI1* variant carriers. Therefore, the following disease entities have been split and curated separately: 1) autosomal recessive congenital myopathy expressed as a hypocontractile phenotype with early-onset; and 2) autosomal dominant congenital myopathy expressed as a hypercontractile phenotype with childhood and adult onset. Evidence supporting this gene-disease relationship include case-level, experimental, and expression data. The initial cohort study by Donkervoort *et al.* identified one splice-site and two missense variants in three probands with childhood onset myopathy with clinical presentations of mainly proximal muscle weakness with varying severity and progression, ptosis, scoliosis, contractures of elbows and hips, severe generalized hypotonia, and presence of nemaline bodies in patient muscle tissue (PMID: 38569017). These probands came from three families, however, disease segregation within each family was limited to one generation. The mechanism of pathogenicity is reported to be loss of function. The gene-disease association is supported by expression data (Uhlen *et al.* PMID: 25613900, Li *et al.* PMID: 36520026) and functional alteration in patient myofiber biopsy (Donkervoort *et al.* PMID: 38569017) which supports a hypocontractile phenotype consistent with a potential loss-of-function mechanism. In summary, there is LIMITED evidence to support the association between *TNNI1* and autosomal recessive congenital myopathy. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease association. This classification was approved by the ClinGen Congenital Myopathy Gene Curation Expert Panel on the meeting date November 24, 2025 (SOP Version 11).
Inheritance Pattern: AD
Disease ID:MONDO:0018958
Submitter: ClinGen
*TNNI1* was first reported in relation to autosomal dominant congenital myopathy in 2024 (Donkervoort *et al.* PMID: 38569017). Per criteria outlined by the ClinGen Lumping and Splitting guidelines, we found differences in inheritance pattern and phenotypic variability for *TNNI1* variant carriers. Therefore, the following disease entities have been split and curated separately: 1) autosomal recessive congenital myopathy expressed as a hypocontractile phenotype with early-onset; and 2) autosomal dominant congenital myopathy expressed as a hypercontractile phenotype with childhood and adult onset. Evidence supporting this gene-disease relationship include case-level, experimental, and expression data. The initial cohort study by Donkervoort *et al.* identified one missense variant and one in-frame deletion variant in two probands with nemaline myopathy with clinical presentations of mainly muscle cramping, myalgias, stiffness, reduced exercise endurance, fatigue, difficulty swallowing, and presence of nemaline bodies in patient muscle tissue (PMID: 38569017). The mechanism of pathogenicity is reported to be gain of function. In addition, Nishimori *et al.* reported a *TNNI1* nonsense variant in a family with proximal arthrogryposis, joint contractures, serum high creatinine kinase levels, abnormal muscle pathology, and without muscle weakness (PMID: 34934811). Disease segregation within the families reported by Donkervoort “et al.” and Nishimori *et al.* was limited to two generations. The gene-disease association is supported by expression data (Uhlen *et al.* PMID: 25613900, Li *et al.* PMID: 36520026) and functional alteration in patient myofiber biopsy (Donkervoort *et al.* PMID: 38569017) which supports a hypercontractile phenotype consistent with a potential gain-of-function mechanism, however, direct functional evidence and investigation is still required. In summary, there is LIMITED evidence to support the association between *TNNI1* and autosomal dominant congenital myopathy. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease association. This classification was approved by the ClinGen Congenital Myopathy Gene Curation Expert Panel on the meeting date November 24, 2025 (SOP Version 11).
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TNNI1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003281.4. 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 | 1 | 2 | |||
| missense | 26 | 26 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 27 | 1 | 0 | 28 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003272.3 | 7 | MANE Select | |
| Ensembl | ENSP00000354488.4 | 7 | MANE Select | |
| Ensembl | ENSP00000337022.4 | 7 | Standard | |
| Ensembl | ENSP00000337022.4 | 7 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| tnni1b | Danio rerio | Structure: atrium Quality: morphology abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Disopyramide Action Pathway
- Procainamide (Antiarrhythmic) Action Pathway
- Phenytoin (Antiarrhythmic) Action Pathway
- Fosphenytoin (Antiarrhythmic) Action Pathway
- Bopindolol Action Pathway
Biological Process
- muscle contraction
- regulation of striated muscle contraction
- transition between fast and slow fiber
- muscle filament sliding
- ventricular cardiac muscle tissue morphogenesis
Molecular Function
- actin binding
- protein binding
- metal ion binding
Cellular Component
- cytosol
- troponin complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000361379
- Coding exons
- 7
- Length
- 25370
- Individuals with no LoFs
- 125737
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 11
- Defined
- 125748
- p
- 0.0000437
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.65 | 74 | 126 | 0.587 | 0.00000877 | 1208 |
| Missense (PolyPhen) | 25 | 55.241 | 0.45256 | 569 | ||
| Synonymous | 0.992 | 39 | 47.7 | 0.817 | 0.00000305 | 374 |
| Loss of Function | 1.07 | 8 | 12.0 | 0.666 | 6.55e-7 | 140 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000058 | 0.000058 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000054 | 0.000053 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Troponin I is the inhibitory subunit of troponin, the thin filament regulatory complex which confers calcium-sensitivity to striated muscle actomyosin ATPase activity.;
Recessive Scores
- pRec
- 0.192
Intolerance Scores
- LoFtool
- 0.288
- RVIS EVS
- 0.24
- RVIS percentile EVS
- 68.98
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.879
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |