TCP11
protein-codingt-complex 11
Gene summary
Involved in germ cell development. Located in acrosomal vesicle and sperm flagellum. [provided by Alliance of Genome Resources, Jul 2025]
- D6S230E
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~30.5 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 TCP11 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001370687.1. 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 | 51 | 51 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 51 | 0 | 0 | 51 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001357616.1 | 9 | MANE Select | |
| Ensembl | ENSP00000308708.6 | 9 | MANE Select | |
| RefSeq | NP_001248746.2 | 9 | Standard | |
| RefSeq | NP_001248747.1 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- multicellular organism development
- spermatogenesis
- protein kinase A signaling
- cell differentiation
- regulation of cAMP-mediated signaling
Cellular Component
- acrosomal vesicle
- integral component of membrane
- sperm flagellum
- sperm midpiece
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000311875
- Coding exons
- 10
- Length
- 30540
- Individuals with no LoFs
- 125627
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 120
- Defined
- 125747
- p
- 0.000477
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.872 | 231 | 271 | 0.851 | 0.0000139 | 3360 |
| Missense (PolyPhen) | 47 | 81.222 | 0.57866 | 1150 | ||
| Synonymous | 1.16 | 91 | 106 | 0.857 | 0.00000544 | 1015 |
| Loss of Function | 1.41 | 14 | 21.0 | 0.667 | 9.52e-7 | 273 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.000062 | 0.000062 | rare |
| Latino/Admixed American | 0.00049 | 0.00049 | rare |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.0013 | 0.0013 | notable |
| Finnish | 0.000095 | 0.000092 | rare |
| European (Non-Finnish) | 0.00066 | 0.00063 | rare |
| South Asian | 0.000065 | 0.000033 | rare |
| Other | 0.00036 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Plays a role in the process of sperm capacitation and acrosome reactions. Probable receptor for the putative fertilization-promoting peptide (FPP) at the sperm membrane that may modulate the activity of the adenylyl cyclase cAMP pathway. {ECO:0000250|UniProtKB:Q01755}.;
Recessive Scores
- pRec
- 0.0873
Intolerance Scores
- LoFtool
- 0.933
- RVIS EVS
- 0.55
- RVIS percentile EVS
- 81.55
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.749
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |