TRABD2A
protein-codingTraB domain containing 2A
Gene summary
Enables Wnt-protein binding activity and metalloendopeptidase activity. Involved in negative regulation of Wnt signaling pathway and proteolysis. Located in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
- C2orf89
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~85.4 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 TRABD2A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001277053.2. 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 | 0 | |||||
| missense | 84 | 7 | 91 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 85 | 7 | 0 | 92 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001263982.1 | 7 | MANE Select | |
| Ensembl | ENSP00000387075.2 | 7 | MANE Select | |
| RefSeq | NP_001074293.1 | 6 | Standard | |
| RefSeq | NP_001294907.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- proteolysis
- Wnt signaling pathway
- negative regulation of Wnt signaling pathway
- positive regulation of protein oligomerization
- head development
Molecular Function
- endopeptidase activity
- metalloendopeptidase activity
- Wnt-protein binding
- metal ion binding
Cellular Component
- integral component of plasma membrane
- membrane
- integral component of organelle membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000335459
- Coding exons
- 6
- Length
- 85359
- Individuals with no LoFs
- 124609
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 47
- Defined
- 124656
- p
- 0.000189
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.454 | 254 | 275 | 0.923 | 0.0000172 | 2917 |
| Missense (PolyPhen) | 80 | 96.101 | 0.83246 | 1169 | ||
| Synonymous | 0.359 | 104 | 109 | 0.956 | 0.00000608 | 948 |
| Loss of Function | 0.661 | 15 | 18.0 | 0.832 | 0.00000103 | 194 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00013 | 0.00013 | rare |
| Latino/Admixed American | 0.00055 | 0.00055 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00046 | 0.00045 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00013 | 0.00013 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Metalloprotease that acts as a negative regulator of the Wnt signaling pathway by mediating the cleavage of the 8 N- terminal residues of a subset of Wnt proteins. Following cleavage, Wnt proteins become oxidized and form large disulfide-bond oligomers, leading to their inactivation. Able to cleave WNT3A, WNT5, but not WNT11. Required for head formation. {ECO:0000269|PubMed:22726442}.;
Intolerance Scores
- RVIS EVS
- 0.22
- RVIS percentile EVS
- 68.38
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |