TRIP13
protein-codingthyroid hormone receptor interactor 13, the group of AAA ATPases
Gene summary
This gene encodes a protein that interacts with thyroid hormone receptors, also known as hormone-dependent transcription factors. The gene product interacts specifically with the ligand binding domain. This gene is one of several that may play a role in early-stage non-small cell lung cancer. [provided by RefSeq, Oct 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~26.5 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0054736
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0033565
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0033565
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0054736
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0054736
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0033565
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AD
Disease ID:MONDO:0000141
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0044626
Submitter: Franklin by Genoox
Identified homozygous and compound heterozygous missense pathogenic variants in TRIP13 responsible for female infertility mainly characterized by oocyte meiotic arrest in five individuals from four independent families. In vitro and in vivo studies showed that the identified variants reduced the protein abundance of TRIP13 and caused its downstream molecule, HORMAD2, to accumulate in HeLa cells and in proband-derived lymphoblastoid cells. https://doi.org/10.1016/j.ajhg.2020.05.001
Inheritance Pattern: AD
Disease ID:MONDO:0019004
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0054736
Submitter: PanelApp Australia
Clinical Genomic Database (CGD)
Manifestation: Craniofacial; Musculoskeletal; Neurologic; Obstetric; Oncologic; Ophthalmologic
Intervention: Oncologic
Rationale: Individuals have been descriebd as susceptible to early-onset Wilms tumor, and awareness may allow early diagnosis and management
Comments: Increased susceptibility to other types of cancer has been suggested
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to TRIP13 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004237.4. 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 | 5 | 48 | 53 | |||
| missense | 3 | 1 | 78 | 4 | 1 | 87 |
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | 2 | |||
| splice donor/acceptor (+/-2bp) | 1 | 2 | 2 | 5 | ||
| Total | 6 | 4 | 85 | 52 | 1 | 148 |
Highest pathogenic variant AF is 0.00001094574
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004228.1 | 13 | MANE Select | |
| Ensembl | ENSP00000166345.3 | 13 | MANE Select | |
| RefSeq | NP_001159732.1 | 9 | Standard | |
| Ensembl | ENSP00000427528.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- miR-targeted genes in epithelium - TarBase
- miR-targeted genes in lymphocytes - TarBase
Biological Process
- oocyte maturation
- double-strand break repair
- transcription by RNA polymerase II
- mitotic spindle assembly checkpoint
- synaptonemal complex assembly
Molecular Function
- transcription coregulator activity
- protein binding
- ATP binding
- identical protein binding
Cellular Component
- male germ cell nucleus
- nucleus
- chromosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000166345
- Coding exons
- 13
- Length
- 26715
- Individuals with no LoFs
- 125742
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 6
- Defined
- 125748
- p
- 0.0000239
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.32 | 141 | 243 | 0.581 | 0.0000131 | 2832 |
| Missense (PolyPhen) | 14 | 61.596 | 0.22729 | 688 | ||
| Synonymous | -0.907 | 113 | 101 | 1.11 | 0.00000619 | 830 |
| Loss of Function | 4.28 | 2 | 25.2 | 0.0795 | 0.00000132 | 279 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000027 | 0.000026 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a key role in chromosome recombination and chromosome structure development during meiosis. Required at early steps in meiotic recombination that leads to non-crossovers pathways. Also needed for efficient completion of homologous synapsis by influencing crossover distribution along the chromosomes affecting both crossovers and non-crossovers pathways. Also required for development of higher-order chromosome structures and is needed for synaptonemal-complex formation. In males, required for efficient synapsis of the sex chromosomes and for sex body formation. Promotes early steps of the DNA double- strand breaks (DSBs) repair process upstream of the assembly of RAD51 complexes. Required for depletion of HORMAD1 and HORMAD2 from synapsed chromosomes (By similarity). Plays a role in mitotic spindle assembly checkpoint (SAC) activation (PubMed:28553959). {ECO:0000250|UniProtKB:Q3UA06, ECO:0000269|PubMed:28553959}.;
- Disease
- DISEASE: Mosaic variegated aneuploidy syndrome 3 (MVA3) [MIM:617598]: A form of mosaic variegated aneuploidy syndrome, a severe disorder characterized by mosaic aneuploidies, predominantly trisomies and monosomies, involving multiple different chromosomes and tissues. Affected individuals typically present with severe intrauterine growth retardation and microcephaly. Eye anomalies, mild dysmorphism, variable developmental delay, and a broad spectrum of additional congenital abnormalities and medical conditions may also occur. The risk of malignancy is high, with rhabdomyosarcoma, Wilms tumor and leukemia reported in several cases. MVA3 inheritance is autosomal recessive. {ECO:0000269|PubMed:28553959}. Note=The disease is caused by mutations affecting the gene represented in this entry. MVA3 is caused by biallelic mutations in the TRIP13 gene.;
Recessive Scores
- pRec
- 0.123
Intolerance Scores
- LoFtool
- 0.108
- RVIS EVS
- -0.23
- RVIS percentile EVS
- 37.32
Essentials
- Essential (CRISPR)
- E
- Essential (CRISPR2)
- E
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.992
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |