TPM4

protein-coding

tropomyosin 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

NM_003290.3

Inheritance

AD

ClinVar variants

P:3U:27B:4

Top phenotype

Bleeding disorder, platelet-type, 25

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr19:16,067,021-16,103,005

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~36.0 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

TPM4-related platelet disorderMODERATE

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.

bleeding disorder, platelet-type, 25STRONG

Inheritance Pattern: AD

Disease ID:MONDO:0957580

Submitter: PanelApp Australia

autosomal dominant macrothrombocytopeniaSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0015372

Submitter: Orphanet

Clinical Genomic Database (CGD)

Bleeding disorder, platelet-type, 25AD

Manifestation: Hematologic

Intervention: Hematologic

Rationale: The condition may involve bleeding tendency, and awareness may be beneficial related to prevention and management of bleeding episodes

Refs: 27479822; 28134622; 34758189; 35170221Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TPM4 variants in ClinVar

5 Conditions Cataloged
not specifiedTotal: 21
not providedTotal: 8
Bleeding disorder, platelet-type, 25Total: 4
ThrombocytopeniaTotal: 1
Abnormal bleedingTotal: 1

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
3
clinvar
1
clinvar
5
missense
1
clinvar
23
clinvar
24
nonsense
2
clinvar
2
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
3
clinvar
3
Total21273134

Highest pathogenic variant AF is 0.000007444501

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_003290.3RefSeqNP_003281.18MANE Select
ENST00000643579.2EnsemblENSP00000495347.18MANE Select
NM_001145160.2RefSeqNP_001138632.19Standard
NM_001367836.1RefSeqNP_001354765.19Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
tpm4aDanio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.9511271610.7890.000009321865
Missense (PolyPhen)4160.8340.67396762
Synonymous0.8885463.00.8580.00000378493
Loss of Function3.05418.00.2239.52e-7227

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish00.0absent
East Asian00.0absent
Finnish0.0000460.000046rare
European (Non-Finnish)0.0000800.000079rare
South Asian0.0000370.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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