TTR
protein-codingtransthyretin, the group of Gla domain containing
Gene summary
This gene encodes one of the three prealbumins, which include alpha-1-antitrypsin, transthyretin and orosomucoid. The encoded protein, transthyretin, is a homo-tetrameric carrier protein, which transports thyroid hormones in the plasma and cerebrospinal fluid. It is also involved in the transport of retinol (vitamin A) in the plasma by associating with retinol-binding protein. The protein may also be involved in other intracellular processes including proteolysis, nerve regeneration, autophagy and glucose homeostasis. Mutations in this gene are associated with amyloid deposition, predominantly affecting peripheral nerves or the heart, while a small percentage of the gene mutations are non-amyloidogenic. The mutations are implicated in the etiology of several diseases, including amyloidotic polyneuropathy, euthyroid hyperthyroxinaemia, amyloidotic vitreous opacities, cardiomyopathy, oculoleptomeningeal amyloidosis, meningocerebrovascular amyloidosis and carpal tunnel syndrome. [provided by RefSeq, Aug 2017]
- PALB
- CTS1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~41.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AD
Disease ID:MONDO:0000992
Submitter: Genomics England PanelApp
Inheritance Pattern: AD
Disease ID:MONDO:0017132
Submitter: ClinGen
The TTR gene has been associated with amyloidosis, an autosomal dominant syndromic disorder characterized by deposition of extracellular transthyretin amyloid deposits throughout the body. Of note, autosomal recessive inheritance has been reported. Being a syndrome, individuals with TTR- related amyloidosis can present with multi-systemic phenotypes including, polyneuropathy, carpal tunnel syndrome, cardiomyopathy, gastrointestinal features, autonomic insufficiency, and renal insufficiency. Familial amyloidosis was first described in 1952 (Andrade et al.; PMID 12978172), but it was not until 1984 (Saraiva et al.; PMID 6736244) that TTR was discovered as the causative gene responsible for this initial report of familial amyloidosis. There are >100 known mutations in TTR reported in humans world-wide as documented in Mutations in Hereditary Amyloidosis Registry (http://www.amyloidosismutations.com) and the Indiana University- Purdue University Indianapolis (IUPUI), USA Amyloidosis Research group site at (http://www.iupui.edu/~amyloid/home.html). All reported mutations are missense (Rowczenio et al., 2014). Multiple cases are reported in the literature but the maximum score for genetic evidence (12 pts) has been reached. The mechanism for disease is gain of function, as mutation causes either tetramer dissociation or monomer denaturation, which both contribute to the formation of amyloid fibrils in tissue (Sekijima, 2015; PMID 25604431). Note, wild-type ATTR (wtATTR), the protein product of the TTR gene, can cause amyloidosis (senile cardiac amyloidosis) on its own, but this form is age-dependent, and often occurs at a much greater age of onset than individuals who harbor a pathogenic variant in TTR. This gene-disease association is supported by the function of the gene product, decreased myocyte functional activity in non-patient cells treated with fibril forming TTR, multiple animal models, rescue experiments, and studies of the clinical impact of anti-sense-oligonucleotides (ASOs) for the treatment of amyloidosis in humans (http://ttrstudy.com). In summary, TTR is definitively associated with Amyloidosis. This association has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. Lumping and Splitting: Per criteria outlined by the ClinGen Lumping and Splitting Working Group, we found that no difference in molecular mechanism underlies the two disease entities: (1) Amyloidosis, hereditary, transthyretin-related (MIM:105210), and (2) Carpal tunnel syndrome, familial (MIM:115430). Furthermore, carpal tunnel syndrome is often a presenting phenotype that occurs in hereditary amyloidosis (MIM:105210). Therefore, the two entities (MIM:105210 and MIM:115430) have been lumped into one disease entity, Hereditary ATTR amyloidosis. Data on the occurrence of hypertrophic cardiomyopathy (HCM) in individuals with Hereditary ATTR amyloidosis was collected by the Hypertrophic Cardiomyopathy Gene Curation Committee (subgroup of the Cardiovascular Working Group). Some individuals with Hereditary ATTR amyloidosis present with features of hypertrophic cardiomyopathy (HCM) and/or restrictive cardiomyopathy (RCM). The prevalence of HCM and/or RCM in Hereditary ATTR amyloidosis is high but exact percentages have not been accurately defined due the high prevalence of HCM and RCM (~25%) development in senile cardiac amyloidosis, which occurs due to accumulation of wildtype TTR accumulation in the heart with age (Galant et al., 2017 PMID 28213611; Meier-Ewert et al., 2011 PMID 21989745; Perlini et al, 2016 PMID 27900617; Ruberg and Berk, 2012 PMID 22949539). Several variants including TTR-V30M, TTR-T60A, and TTR-V122L are the most commonly associated with cardiac amyloidosis (Siddiqi and Ruberg, 2017 PMID 28739313). Additionally, the Charcot-Marie-Tooth Gene Curation Working Group reviewed the subtype of individuals that present with features of polyneuropathy, those individuals typically developing an axonal, length-dependent, predominantly sensory and autonomic neuropathy or small fiber neuropathy in the early course, which rapidly progresses involving motor nerves as well. For the neuropathy sub-phenotype, the current literature provides additional evidence including further neuropathy cases associated to various TTR mutations such as p.Val50Met (PMIDs: 8071954, 19180884, 24101130) and p.Leu75Pro (1351039, 7910950, 31319424) with variant-based functional studies ranging from urea-assays (PMID: 12351683) to mouse models (PMIDs: 9095004, 12351683). Functional evidence further supports the gene-disease relationship for neuropathy, including expression studies (PMID: 28335735), nerve tissue based cell cultures (PMIDs: 11567048, 18983977, 14981241), and rescue experiments including three successful phase 3 clinical trials (PMIDs: 22843282, 30145929, 29972753)
Inheritance Pattern: AD
Disease ID:MONDO:0007100
Submitter: Ambry Genetics
Inheritance Pattern: AD
Disease ID:MONDO:0020730
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0971004
Submitter: G2P
Inheritance Pattern: AD
Disease ID:MONDO:0007100
Submitter: Orphanet
Inheritance Pattern: AD
Disease ID:MONDO:0007100
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0971004
Submitter: PanelApp Australia
Inheritance Pattern: AD
Disease ID:MONDO:0019441
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Endocrine; Gastrointestinal; Musculoskeletal; Neurologic; Ophthalmologic; Renal
Intervention: Cardiovascular; Endocrine; Gastrointestinal; Neurologic
Rationale: In Hereditary amyloidosis, surveillance for cardiovascular sequelae (which can include arrhythmias), and earlier treatment (eg, with pacemaker placement) can be beneficial, and liver transplantation may be beneficial especially early in the disease course; Therapies involving transthyretin stabilization, RNA interference, or inhibtion of the hepatic production of transthyretin protein may be beneficial, especially in early stages of disease; In Dystransthyretinemic hyperthyroxinemia, diagnosis may be important in order to avoid unecessary treatment (eg, thyroid ablation)
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TTR variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_000371.4. 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 | 3 | 66 | 4 | 73 | ||
| missense | 53 | 93 | 95 | 7 | 3 | 251 |
| nonsense | 5 | 1 | 6 | |||
| start loss | 0 | |||||
| frameshift | 9 | 9 | ||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 53 | 93 | 118 | 74 | 7 | 345 |
Highest pathogenic variant AF is 0.0008878111
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_000362.1 | 4 | MANE Select | |
| Ensembl | ENSP00000237014.4 | 4 | MANE Select | |
| Ensembl | ENSP00000477599.2 | 3 | Standard | |
| Ensembl | ENSP00000477599.2 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Thyroid hormone synthesis - Homo sapiens (human)
- Signaling by GPCR
- Neutrophil degranulation
- Signal Transduction
- Metabolism of fat-soluble vitamins
Biological Process
- retinoid metabolic process
- purine nucleobase metabolic process
- regulation of signaling receptor activity
- extracellular matrix organization
- retinol metabolic process
Molecular Function
- hormone activity
- protein binding
- identical protein binding
- protein heterodimerization activity
- thyroid hormone binding
Cellular Component
- extracellular region
- extracellular space
- protein-containing complex
- azurophil granule lumen
- extracellular exosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000237014
- Coding exons
- 4
- Length
- 7286
- Individuals with no LoFs
- 125741
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125744
- p
- 0.0000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.01 | 57 | 83.0 | 0.687 | 0.00000464 | 934 |
| Missense (PolyPhen) | 17 | 28.783 | 0.59064 | 343 | ||
| Synonymous | 0.433 | 30 | 33.2 | 0.904 | 0.00000190 | 312 |
| Loss of Function | 1.94 | 1 | 6.22 | 0.161 | 3.52e-7 | 69 |
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 | 0.0 | absent |
| European (Non-Finnish) | 0.000026 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Thyroid hormone-binding protein. Probably transports thyroxine from the bloodstream to the brain. {ECO:0000269|PubMed:3714052}.;
- Disease
- DISEASE: Amyloidosis, transthyretin-related (AMYL-TTR) [MIM:105210]: A hereditary generalized amyloidosis due to transthyretin amyloid deposition. Protein fibrils can form in different tissues leading to amyloid polyneuropathies, amyloidotic cardiomyopathy, carpal tunnel syndrome, systemic senile amyloidosis. The disease includes leptomeningeal amyloidosis that is characterized by primary involvement of the central nervous system. Neuropathologic examination shows amyloid in the walls of leptomeningeal vessels, in pia arachnoid, and subpial deposits. Some patients also develop vitreous amyloid deposition that leads to visual impairment (oculoleptomeningeal amyloidosis). Clinical features include seizures, stroke-like episodes, dementia, psychomotor deterioration, variable amyloid deposition in the vitreous humor. {ECO:0000269|PubMed:10036587, ECO:0000269|PubMed:10071047, ECO:0000269|PubMed:10211412, ECO:0000269|PubMed:10436378, ECO:0000269|PubMed:10439117, ECO:0000269|PubMed:10611950, ECO:0000269|PubMed:10627135, ECO:0000269|PubMed:10694917, ECO:0000269|PubMed:10842705, ECO:0000269|PubMed:10842718, ECO:0000269|PubMed:10882995, ECO:0000269|PubMed:11243784, ECO:0000269|PubMed:11445644, ECO:0000269|PubMed:11866053, ECO:0000269|PubMed:12050338, ECO:0000269|PubMed:12403615, ECO:0000269|PubMed:12557757, ECO:0000269|PubMed:12771253, ECO:0000269|PubMed:1301926, ECO:0000269|PubMed:1351039, ECO:0000269|PubMed:1362222, ECO:0000269|PubMed:1436517, ECO:0000269|PubMed:1517749, ECO:0000269|PubMed:1520326, ECO:0000269|PubMed:1520336, ECO:0000269|PubMed:15214015, ECO:0000269|PubMed:15217993, ECO:0000269|PubMed:1544214, ECO:0000269|PubMed:15478468, ECO:0000269|PubMed:1570831, ECO:0000269|PubMed:15735344, ECO:0000269|PubMed:16185074, ECO:0000269|PubMed:1656975, ECO:0000269|PubMed:16627944, ECO:0000269|PubMed:1734866, ECO:0000269|PubMed:17453626, ECO:0000269|PubMed:17503405, ECO:0000269|PubMed:17577687, ECO:0000269|PubMed:17635579, ECO:0000269|PubMed:19167329, ECO:0000269|PubMed:1932142, ECO:0000269|PubMed:2046936, ECO:0000269|PubMed:2161654, ECO:0000269|PubMed:23317988, ECO:0000269|PubMed:2363717, ECO:0000269|PubMed:2891727, ECO:0000269|PubMed:3022108, ECO:0000269|PubMed:3135807, ECO:0000269|PubMed:3722385, ECO:0000269|PubMed:3818577, ECO:0000269|PubMed:6487335, ECO:0000269|PubMed:6583672, ECO:0000269|PubMed:6651852, ECO:0000269|PubMed:7655883, ECO:0000269|PubMed:7850982, ECO:0000269|PubMed:7910950, ECO:0000269|PubMed:7914929, ECO:0000269|PubMed:7923855, ECO:0000269|PubMed:8019560, ECO:0000269|PubMed:8038017, ECO:0000269|PubMed:8081397, ECO:0000269|PubMed:8095302, ECO:0000269|PubMed:8133316, ECO:0000269|PubMed:8257997, ECO:0000269|PubMed:8352764, ECO:0000269|PubMed:8382610, ECO:0000269|PubMed:8428915, ECO:0000269|PubMed:8579098, ECO:0000269|PubMed:8990019, ECO:0000269|PubMed:9066351, ECO:0000269|PubMed:9605286, ECO:0000269|PubMed:9733771, ECO:0000269|Ref.90}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Hyperthyroxinemia, dystransthyretinemic (DTTRH) [MIM:145680]: A condition characterized by elevation of total and free thyroxine in healthy, euthyroid persons without detectable binding protein abnormalities. {ECO:0000269|PubMed:1979335}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Carpal tunnel syndrome 1 (CTS1) [MIM:115430]: A condition characterized by entrapment of the median nerve within the carpal tunnel. Symptoms include burning pain and paresthesias involving the ventral surface of the hand and fingers which may radiate proximally. Impairment of sensation in the distribution of the median nerve and thenar muscle atrophy may occur. This condition may be associated with repetitive occupational trauma, wrist injuries, amyloid neuropathies, rheumatoid arthritis. {ECO:0000269|PubMed:8309582}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.845
Intolerance Scores
- LoFtool
- 0.0557
- RVIS EVS
- 0.5
- RVIS percentile EVS
- 79.89
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.869
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |