TRDN
protein-codingtriadin
Gene summary
This gene encodes an integral membrane protein found in skeletal and cardiac muscle. The encoded protein plays a role in skeletal muscle excitation-contraction coupling as part of the calcium release complex and is required for normal skeletal muscle strength. This protein indirectly links triads and microtubules in skeletal muscle. Mutations in this gene are associated with cardiac arrythmia syndrome and some variants in this gene may be associated with sudden cardiac death. [provided by RefSeq, May 2022]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~420.9 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0014191
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0002442
Submitter: ClinGen
TRDN encodes Triadin, a protein important for calcium-release regulation from the sarcoplasmic reticulum. Evidence for involvement of TRDN in LQTS is based mainly on a single publication using exome sequencing to investigate a genotype-negative LQTS case with clinical findings concordant with autosomal recessive or sporadic inheritance (PMID 25922419). Following identification of homozygous frameshift variant in TRDN, 4 other patients with homozygous or compound heterozygous frameshift variants in TRDN were identified in a cohort of 33 unrelated genotype-negative LQTS patients. All cases presented during early childhood (up to the age of 3 years) with QT prolongation, negative T waves in precordial leads (figure 2) and exercise-induced arrhythmias, although typical torsades de pointes (TdP) was demonstrated only in one case. Experimental evidence demonstrated that TRDN loss of function may lead to arrhythmogenesis but did not specifically show prolongation of repolarization which is the hallmark of LQTS. Accordingly, there was a debate within the panel as to whether the TRDN-related cardiac phenotype should be classified as catecholaminergic polymorphic ventricular tachycardia or as a unique syndrome, referred in the literature as triadin knockout syndrome (TKOS) (PMID 26200674). Because QT prolongation was the most easily discernable abnormality it was decided to consider these cases as having an atypical LQTS phenotype. Furthermore, it was agreed that there was strong evidence for TRDN’s disease association. Note: All LQTS genes were curated by 3 separate blinded teams. The evidence and scores reached by these 3 teams was reviewed by the LQTS Clinical Domain Working Group. The classification and summary presented here is the conclusion of this Working Group's analysis according to evidence teams' efforts. For a detailed discussion of this group's work and the scores of all 3 teams please see "Adler et al. An International, Multicentered, Evidence-Based Reappraisal of Genes Reported to Cause Congenital Long QT Syndrome. Circulation 2020;141(6):418-428. doi: 10.1161/CIRCULATIONAHA.119.043132”
Inheritance Pattern: AR
Disease ID:MONDO:0017990
Submitter: ClinGen
TRDN was evaluated for autosomal recessive catecholaminergic polymorphic ventricular tachycardia (CPVT). TRDN encodes Triadin, a protein important for calcium-release regulation from the sarcoplasmic reticulum. Biallelic loss of function variants in TRDN have been described in CPVT patients in a number of studies (Roux-Buisson et al, 2012, PMID:22422768; Rooryck et al, 2015, PMID:26200674; Walsh et al, 2016, PMID:26768964), including nonsense (p.Gln205Ter, p.Glu168Ter), frameshift (c.53_56del), intronic (c.22+29A>G, with effect on splicing functionally proven) and missense (p.Thr59Arg, the mutant protein was confirmed to be degraded in COS-7 cells and after transfection into knockout mice) variants. An additional report described a homozygous deletion of TRDN exon 2 in an infant who suffered cardiac arrest and subsequent arrhythmia episodes, but this case was scored with only one point due to uncertainty about the phenotype and the additional presence of a RYR2 variant of uncertain significance in this patient (O'Callaghan et al, 2018, PMID:30479949). Biallelic truncating variants in TRDN have also been reported in patients with Long QT syndrome, and the LQTS Gene Curation Expert Panel have previously classified TRDN as having strong evidence for association with LQTS, though with an atypical LQTS phenotype. The variable and atypical phenotypes associated with so-called “Triadin knockout syndrome” should therefore be taken into account when interpreting patients with TRDN biallelic loss of function variants. The association of TRDN with CPVT is also supported by substantial experimental evidence, including expression in heart tissue (Cacheux et al, 2019, PMID:31607542), protein interaction with RYR2 and CASQ2 (Guo et al, 1996, PMID:8550602) and relevant biochemical function in regulating the contractile properties of the heart (Kirchhefer et al, 2001, PMID:11069905). Additionally, knockout mice are directly relevant to the genotypes observed in CPVT patients with TRDN variants, with several studies demonstrating a relevant CPVT phenotype in knockout mice for non-human model organism (e.g. Cacheux et al, 2019, PMID:31607542; Chopra et al, 2009, PMID:19383796) and functional alteration in non-patient cells derived from these mouse knockouts (Chopra et al, 2009, PMID:19383796). Partial rescue of the CPVT phenotype has also been observed in knockout mice treated with AAV2/9 virus encoding rat TRDN isoform Trisk32 (Cacheux et al, 2019, PMID:31607542). In summary, TRDN variants are definitively associated with autosomal recessive CPVT. Note: All CPVT genes were curated by 3 separate blinded teams. The evidence and scores reached by these 3 teams was reviewed by the CPVT Gene Curation Expert Panel (GCEP). The classification and summary presented here is the conclusion of this GCEP's analysis according to evidence teams' efforts. This classification was approved by the ClinGen Catecholaminergic Polymorphic Ventricular Tachycardia Gene Curation Expert Panel on 20th January, 2021 (SOP Version 7).
Inheritance Pattern: AR
Disease ID:MONDO:0014191
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0014191
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0014191
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0019171
Submitter: G2P
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Musculoskeletal; Neurologic
Intervention: Cardiovascular
Rationale: Individuals may present with severe cardiac manifestations, including arrhythmias, syncope, and sudden death, and surveillance, preventive measures (eg, including avoidance of dangerous or excacerbating factors), and treatment (eg, including interventions such as medical treatment with beta-blockers or ICD placement) may allow early and beneficial management, which may decrease morbidity and mortality
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TRDN variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_006073.4. 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 | 11 | 201 | 212 | |||
| missense | 1 | 3 | 446 | 68 | 1 | 519 |
| nonsense | 5 | 7 | 22 | 34 | ||
| start loss | 1 | 1 | ||||
| frameshift | 15 | 14 | 20 | 1 | 50 | |
| splice donor/acceptor (+/-2bp) | 2 | 19 | 50 | 71 | ||
| Total | 24 | 43 | 549 | 270 | 1 | 887 |
Highest pathogenic variant AF is 0.00032250062
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_006064.2 | 41 | MANE Select | |
| Ensembl | ENSP00000333984.5 | 41 | MANE Select | |
| RefSeq | NP_001238916.1 | 21 | Standard | |
| RefSeq | NP_001242949.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Stimuli-sensing channels
- Ion channel transport
- Ion homeostasis
- Transport of small molecules
- Cardiac conduction
Biological Process
- cellular calcium ion homeostasis
- muscle contraction
- response to bacterium
- regulation of cell communication by electrical coupling
- regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum
Molecular Function
- signaling receptor binding
- protein binding
- protein binding, bridging
- ion channel binding
Cellular Component
- endoplasmic reticulum
- cytosol
- plasma membrane
- junctional sarcoplasmic reticulum membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000398178
- Coding exons
- 41
- Length
- 420756
- Individuals with no LoFs
- 124508
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 127
- Defined
- 124637
- p
- 0.000518
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0770 | 294 | 290 | 1.01 | 0.0000136 | 4687 |
| Missense (PolyPhen) | 60 | 59.054 | 1.016 | 1102 | ||
| Synonymous | 0.0815 | 93 | 94.0 | 0.989 | 0.00000487 | 1180 |
| Loss of Function | 1.46 | 39 | 50.1 | 0.778 | 0.00000242 | 826 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0014 | 0.0014 | notable |
| Latino/Admixed American | 0.00012 | 0.00012 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00034 | 0.00033 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00055 | 0.00053 | rare |
| South Asian | 0.0013 | 0.0012 | notable |
| Other | 0.00036 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Contributes to the regulation of lumenal Ca2+ release via the sarcoplasmic reticulum calcium release channels RYR1 and RYR2, a key step in triggering skeletal and heart muscle contraction. Required for normal organization of the triad junction, where T-tubules and the sarcoplasmic reticulum terminal cisternae are in close contact (By similarity). Required for normal skeletal muscle strength. Plays a role in excitation- contraction coupling in the heart and in regulating the rate of heart beats. {ECO:0000250|UniProtKB:E9Q9K5, ECO:0000269|PubMed:22422768}.;
- Disease
- DISEASE: Ventricular tachycardia, catecholaminergic polymorphic, 5, with or without muscle weakness (CPVT5) [MIM:615441]: An arrhythmogenic disorder characterized by stress-induced, bidirectional ventricular tachycardia that may degenerate into cardiac arrest and cause sudden death. Patients present with recurrent syncope, or sudden death after physical activity or emotional stress. Some patients have muscle weakness. CPVT5 inheritance is autosomal recessive. {ECO:0000269|PubMed:22422768}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.159
Intolerance Scores
- LoFtool
- 0.861
- RVIS EVS
- 1.98
- RVIS percentile EVS
- 97.61
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.275
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | High | Medium | High |
| Cancer | High | High | High |