TNNI1

protein-coding

troponin 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

NM_003281.4

Inheritance

AD, AR

ClinVar variants

U:27B:1

Top phenotype

TNNI1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr1:201,403,784-201,429,866

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~26.1 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

arthrogryposisMODERATE

Inheritance Pattern: AD

Disease ID:MONDO:0008779

Submitter: PanelApp Australia

childhood-onset nemaline myopathyLIMITED

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).

nemaline myopathyLIMITED

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

3 Conditions Cataloged
not specifiedTotal: 24
TNNI1-related disorderTotal: 2
TNNI1-related congenital myopathyTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
1
clinvar
2
missense
26
clinvar
26
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total00271028
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003281.4RefSeqNP_003272.37MANE Select
ENST00000361379.9EnsemblENSP00000354488.47MANE Select
ENST00000336092.8EnsemblENSP00000337022.47Standard
ENST00000336092.9EnsemblENSP00000337022.47Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
tnni1bDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense1.65741260.5870.000008771208
Missense (PolyPhen)2555.2410.45256569
Synonymous0.9923947.70.8170.00000305374
Loss of Function1.07812.00.6666.55e-7140

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000580.000058rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000540.000053rare
South Asian0.0000330.000033rare
Other0.000330.00033rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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