TPM4
protein-codingtropomyosin 4, the group of Tropomyosins
Gene summary
This gene encodes a member of the tropomyosin family of actin-binding proteins involved in the contractile system of striated and smooth muscles and the cytoskeleton of non-muscle cells. Tropomyosins are dimers of coiled-coil proteins that polymerize end-to-end along the major groove in most actin filaments. They provide stability to the filaments and regulate access of other actin-binding proteins. In muscle cells, they regulate muscle contraction by controlling the binding of myosin heads to the actin filament. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~36.0 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0100487
Submitter: ClinGen
*TPM4* was first reported in relation to inherited thrombocytopenia in 2017 (Pleines et al, PMID: 28134622). TPM4 encodes tropomyosin alpha 4 chain. Tropomyosins are dimers of coiled‐coil proteins that provide stability to the actin filaments in which they bind, regulating access of other actin‐binding proteins. *TPM4*- related platelet disorder (Bleeding Disorder, Platelet Type, 25) is an autosomal dominant platelet disorder characterized by variable thrombocytopenia, increased platelet size, and mild platelet dysfunction. Evidence supporting this gene-disease curation includes case-level data and experimental data. Summary of Case Level Data (4 points): Four unique variants have been reported in humans; two nonsense variants and two missense variants. Variants in this gene have been reported in at least 5 probands in 3 publications (Plienes et al, PMID: 28134622; Stapley et al, PMID: 34758189; Marin-Quilez et al, PMID:35170221). Variants in this gene segregated with disease in an additional 8 family members. Summary of Experimental Data (3 points): This gene disease relationship is supported by an animal model (Pleines et al, PMID: 28134622), Biochemical Function (Stapley et al, PMID: 34758189) and expression studies (Pleines et al, PMID: 28134622). In summary, there is moderate evidence to support this gene-disease relationship. Although more evidence is needed to support a causal role, no convincing evidence has emerged that contradicts the gene-disease relationship. This gene-disease classification was originally approved by the ClinGen Hemostasis and Thrombosis (H/T) Gene Curation Expert Panel on February 3, 2022 and re-evaluated on May 1, 2024. No new scoreable genetic or experimental evidence has emerged since the original curation date and as a result, the classification did not change. The ClinGen H/T expert panel is aware of an additional, unpublished case in which an individual with isolated thrombocytopenia and no family history of platelet or bleeding disorders is noted. The variant, *TPM4* (NM_001145160.1) c.572_574del, p.G191del results in an in-frame deletion of a single amino acid (CA2576659843). At this time, this variant is not scored in this curation.
Inheritance Pattern: AD
Disease ID:MONDO:0957580
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0015372
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Hematologic
Intervention: Hematologic
Rationale: The condition may involve bleeding tendency, and awareness may be beneficial related to prevention and management of bleeding episodes
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TPM4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_003290.3. 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 | 1 | 3 | 1 | 5 | ||
| missense | 1 | 23 | 24 | |||
| nonsense | 2 | 2 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 2 | 1 | 27 | 3 | 1 | 34 |
Highest pathogenic variant AF is 0.000007444501
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_003281.1 | 8 | MANE Select | |
| Ensembl | ENSP00000495347.1 | 8 | MANE Select | |
| RefSeq | NP_001138632.1 | 9 | Standard | |
| RefSeq | NP_001354765.1 | 9 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| tpm4a | Danio rerio | Structure: cardiac muscle cell Quality: absent abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Cardiac muscle contraction - Homo sapiens (human)
- Dilated cardiomyopathy (DCM) - Homo sapiens (human)
- Hypertrophic cardiomyopathy (HCM) - Homo sapiens (human)
- Adrenergic signaling in cardiomyocytes - Homo sapiens (human)
- miR-targeted genes in epithelium - TarBase
Biological Process
- osteoblast differentiation
- muscle contraction
- actin filament organization
- muscle filament sliding
Molecular Function
- calcium ion binding
- protein binding
- structural constituent of muscle
- identical protein binding
- protein homodimerization activity
Cellular Component
- stress fiber
- podosome
- cytosol
- cytoskeleton
- muscle thin filament tropomyosin
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000538887
- Coding exons
- 9
- Length
- 35983
- Individuals with no LoFs
- 125734
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 12
- Defined
- 125746
- p
- 0.0000477
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.951 | 127 | 161 | 0.789 | 0.00000932 | 1865 |
| Missense (PolyPhen) | 41 | 60.834 | 0.67396 | 762 | ||
| Synonymous | 0.888 | 54 | 63.0 | 0.858 | 0.00000378 | 493 |
| Loss of Function | 3.05 | 4 | 18.0 | 0.223 | 9.52e-7 | 227 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.000080 | 0.000079 | rare |
| South Asian | 0.000037 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Binds to actin filaments in muscle and non-muscle cells. Plays a central role, in association with the troponin complex, in the calcium dependent regulation of vertebrate striated muscle contraction. Smooth muscle contraction is regulated by interaction with caldesmon. In non-muscle cells is implicated in stabilizing cytoskeleton actin filaments (By similarity). Binds calcium (PubMed:1836432). {ECO:0000250|UniProtKB:P09495, ECO:0000269|PubMed:1836432}.;
Recessive Scores
- pRec
- 0.204
Intolerance Scores
- LoFtool
- 0.332
- RVIS EVS
- -0.07
- RVIS percentile EVS
- 48.12
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.818
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |