TTC23L
protein-codingtetratricopeptide repeat domain 23 like
Gene summary
Predicted to be involved in response to endoplasmic reticulum stress. Predicted to be located in centrosome; midbody; and spindle. [provided by Alliance of Genome Resources, Jun 2026]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~61.7 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 TTC23L variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_144725.4. 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 | 0 | |||||
| missense | 46 | 2 | 48 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 47 | 2 | 0 | 49 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_653326.3 | 9 | MANE Select | |
| Ensembl | ENSP00000422188.1 | 9 | MANE Select | |
| RefSeq | NP_001304878.1 | 10 | Standard | |
| RefSeq | NP_001373098.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- response to endoplasmic reticulum stress
Molecular Function
- protein binding
Cellular Component
- cytoplasm
- microtubule organizing center
- spindle
- midbody
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000505624
- Coding exons
- 9
- Length
- 60624
- Individuals with no LoFs
- 124116
- Homozygous LoFs
- 3
- Heterozygous LoFs
- 521
- Defined
- 124640
- p
- 0.00210
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.566 | 165 | 187 | 0.883 | 0.00000908 | 2343 |
| Missense (PolyPhen) | 46 | 48.053 | 0.95728 | 644 | ||
| Synonymous | 0.731 | 66 | 74.0 | 0.892 | 0.00000395 | 676 |
| Loss of Function | 0.745 | 18 | 21.8 | 0.828 | 0.00000115 | 257 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0012 | 0.0012 | notable |
| Latino/Admixed American | 0.0010 | 0.0010 | notable |
| Ashkenazi Jewish | 0.0045 | 0.0045 | notable |
| East Asian | 0.0070 | 0.0070 | notable |
| Finnish | 0.00042 | 0.00042 | rare |
| European (Non-Finnish) | 0.00089 | 0.00089 | rare |
| South Asian | 0.0060 | 0.0059 | notable |
| Other | 0.0020 | 0.0020 | notable |
dbNSFP Gene Annotations
Source:
Intolerance Scores
- LoFtool
- 0.831
- RVIS EVS
- 1.73
- RVIS percentile EVS
- 96.56
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.152
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |