TRIP13

protein-coding

thyroid 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

NM_004237.4

Inheritance

AR, AD

ClinVar variants

P:10U:85B:53

Top phenotype

Mosaic variegated aneuploidy syndrome 3

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr5:892,884-919,357

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~26.5 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

mosaic variegated aneuploidy syndrome 3STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0054736

Submitter: G2P

oocyte maturation defect 9STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0033565

Submitter: PanelApp Australia

oocyte maturation defect 9LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0033565

Submitter: Ambry Genetics

mosaic variegated aneuploidy syndrome 3LIMITED

Inheritance Pattern: AR

Disease ID:MONDO:0054736

Submitter: Ambry Genetics

mosaic variegated aneuploidy syndrome 3STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0054736

Submitter: Labcorp Genetics (formerly Invitae)

oocyte maturation defect 9STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0033565

Submitter: Labcorp Genetics (formerly Invitae)

mosaic variegated aneuploidy syndromeSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0000141

Submitter: Orphanet

female infertility due to oocyte meiotic arrestMODERATE

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

kidney Wilms tumorSUPPORTIVE

Inheritance Pattern: AD

Disease ID:MONDO:0019004

Submitter: Orphanet

mosaic variegated aneuploidy syndrome 3MODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0054736

Submitter: PanelApp Australia

Clinical Genomic Database (CGD)

Mosaic variegated aneuploidy syndrome 3AR

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

Refs: 28553959; 32473092Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TRIP13 variants in ClinVar

5 Conditions Cataloged
not providedTotal: 153
not specifiedTotal: 57
TRIP13-related disorderTotal: 27
Mosaic variegated aneuploidy syndrome 3Total: 11
Oocyte maturation defect 9Total: 9

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.

EffectPLPVUSLBBSum
synonymous
5
clinvar
48
clinvar
53
missense
3
clinvar
1
clinvar
78
clinvar
4
clinvar
1
clinvar
87
nonsense
1
clinvar
1
start loss
0
frameshift
1
clinvar
1
clinvar
2
splice donor/acceptor (+/-2bp)
1
clinvar
2
clinvar
2
clinvar
5
Total6485521148

Highest pathogenic variant AF is 0.00001094574

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_004237.4RefSeqNP_004228.113MANE Select
ENST00000166345.8EnsemblENSP00000166345.313MANE Select
NM_001166260.2RefSeqNP_001159732.19Standard
ENST00000513435.1EnsemblENSP00000427528.18Standard

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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.321412430.5810.00001312832
Missense (PolyPhen)1461.5960.22729688
Synonymous-0.9071131011.110.00000619830
Loss of Function4.28225.20.07950.00000132279

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American0.0000290.000029rare
Ashkenazi Jewish0.0000990.000099rare
East Asian00.0absent
Finnish00.0absent
European (Non-Finnish)0.0000270.000026rare
South Asian0.0000330.000033rare
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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