THADA
protein-codingTHADA armadillo repeat containing, the group of Armadillo repeat containing
Gene summary
This gene is the target of 2p21 choromosomal aberrations in benign thyroid adenomas. Single nucleotide polymorphisms (SNPs) in this gene may be associated with type 2 diabetes and polycystic ovary syndrome. The encoded protein is likely involved in the death receptor pathway and apoptosis. [provided by RefSeq, Sep 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~365.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to THADA variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_022065.5. 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 | 2 | 17 | 5 | 24 | ||
| missense | 365 | 21 | 11 | 397 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 9 | 9 | ||||
| Total | 0 | 0 | 377 | 38 | 16 | 431 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_071348.3 | 37 | MANE Select | |
| Ensembl | ENSP00000386088.2 | 37 | MANE Select | |
| RefSeq | NP_001077422.1 | 37 | Standard | |
| RefSeq | NP_001258572.1 | 17 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| thada | Danio rerio | Structure: pancreatic B cell Quality: decreased area abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- tRNA modification in the nucleus and cytosol
- tRNA processing
- Metabolism of RNA
Biological Process
- tRNA methylation
- negative regulation of endoplasmic reticulum calcium ion concentration
- lipid homeostasis
- negative regulation of calcium-transporting ATPase activity
- adaptive thermogenesis
Molecular Function
- protein binding
Cellular Component
- cytosol
- cytoplasmic side of endoplasmic reticulum membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000405006
- Coding exons
- 37
- Length
- 429386
- Individuals with no LoFs
- 124373
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 269
- Defined
- 124643
- p
- 0.00108
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -2.96 | 1225 | 966 | 1.27 | 0.0000491 | 12704 |
| Missense (PolyPhen) | 278 | 228.47 | 1.2168 | 3106 | ||
| Synonymous | -3.71 | 450 | 360 | 1.25 | 0.0000190 | 3683 |
| Loss of Function | 1.80 | 73 | 91.6 | 0.797 | 0.00000437 | 1213 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0012 | 0.0012 | notable |
| Latino/Admixed American | 0.00093 | 0.00087 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.0030 | 0.0030 | notable |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.0011 | 0.0010 | notable |
| South Asian | 0.0013 | 0.0013 | notable |
| Other | 0.0015 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
Recessive Scores
- pRec
- 0.0982
Intolerance Scores
- LoFtool
- 1.00
- RVIS EVS
- 0.45
- RVIS percentile EVS
- 77.98
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.461
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | High | Medium | High |
| Primary Immunodeficiency | High | High | High |
| Cancer | High | High | High |