TANC1
protein-codingtetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1, the group of Ankyrin repeat domain containing|MicroRNA protein coding host genes|Tetratricopeptide repeat domain containing
Gene summary
Predicted to be involved in regulation of postsynapse organization. Predicted to act upstream of or within dendritic spine maintenance; myoblast fusion; and visual learning. Predicted to be located in several cellular components, including axon terminus; neuronal cell body; and postsynaptic density. Predicted to be active in glutamatergic synapse and postsynaptic density, intracellular component. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~264.0 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 TANC1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_033394.3. 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 | 10 | 15 | |||
| missense | 245 | 13 | 3 | 261 | ||
| nonsense | 1 | 1 | ||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 0 | 256 | 23 | 3 | 282 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_203752.2 | 25 | MANE Select | |
| Ensembl | ENSP00000263635.6 | 25 | MANE Select | |
| RefSeq | NP_001139381.1 | 25 | Standard | |
| RefSeq | NP_001336991.1 | 22 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- myoblast fusion
- visual learning
- dendritic spine maintenance
Molecular Function
- protein binding
Cellular Component
- postsynaptic density
- cell junction
- dendrite
- neuronal cell body
- axon terminus
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000263635
- Coding exons
- 25
- Length
- 264025
- Individuals with no LoFs
- 124729
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 73
- Defined
- 124802
- p
- 0.000293
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.23 | 934 | 1.05e+3 | 0.893 | 0.0000609 | 12120 |
| Missense (PolyPhen) | 353 | 446.53 | 0.79054 | 5080 | ||
| Synonymous | 0.243 | 435 | 441 | 0.985 | 0.0000295 | 3800 |
| Loss of Function | 5.71 | 24 | 78.7 | 0.305 | 0.00000422 | 935 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00032 | 0.00032 | rare |
| Latino/Admixed American | 0.00061 | 0.00061 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00023 | 0.00023 | rare |
| European (Non-Finnish) | 0.00031 | 0.00031 | rare |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May be a scaffold component in the postsynaptic density. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.100
Intolerance Scores
- LoFtool
- 0.526
- RVIS EVS
- -1.26
- RVIS percentile EVS
- 5.27
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0503
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |