TCP1
Basic information
Region (hg38): 6:159778498-159789703
Links
Phenotypes
GenCC
Source:
- neurodevelopmental disorder (Strong), mode of inheritance: AD
- intellectual developmental disorder with polymicrogyria and seizures (Moderate), mode of inheritance: AD
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Intellectual developmental disorder with polymicrogyria and seizures | AD | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Neurologic | 39480921 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (56 variants)
- not_provided (4 variants)
- Intellectual_developmental_disorder_with_polymicrogyria_and_seizures (4 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TCP1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030752.3. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
---|---|---|---|---|---|---|
synonymous | 0 | |||||
missense | 54 | 57 | ||||
nonsense | 1 | |||||
start loss | 0 | |||||
frameshift | 6 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
Total | 4 | 0 | 57 | 3 | 0 |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TCP1 | protein_coding | protein_coding | ENST00000321394 | 12 | 11252 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.995 | 0.00473 | 125736 | 0 | 11 | 125747 | 0.0000437 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.60 | 228 | 307 | 0.742 | 0.0000152 | 3649 |
Missense in Polyphen | 32 | 91.91 | 0.34817 | 1180 | ||
Synonymous | -0.935 | 117 | 105 | 1.12 | 0.00000506 | 1110 |
Loss of Function | 4.23 | 2 | 24.7 | 0.0811 | 0.00000123 | 315 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.00 | 0.00 |
Ashkenazi Jewish | 0.0000994 | 0.0000992 |
East Asian | 0.0000554 | 0.0000544 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.0000617 | 0.0000615 |
Middle Eastern | 0.0000554 | 0.0000544 |
South Asian | 0.00 | 0.00 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Component of the chaperonin-containing T-complex (TRiC), a molecular chaperone complex that assists the folding of proteins upon ATP hydrolysis (PubMed:25467444). The TRiC complex mediates the folding of WRAP53/TCAB1, thereby regulating telomere maintenance (PubMed:25467444). As part of the TRiC complex may play a role in the assembly of BBSome, a complex involved in ciliogenesis regulating transports vesicles to the cilia (PubMed:20080638). The TRiC complex plays a role in the folding of actin and tubulin (Probable). {ECO:0000269|PubMed:20080638, ECO:0000269|PubMed:25467444, ECO:0000305}.;
- Pathway
- Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation;Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding;Metabolism of proteins;Chaperonin-mediated protein folding;Formation of tubulin folding intermediates by CCT/TriC;Association of TriC/CCT with target proteins during biosynthesis;Protein folding;Prefoldin mediated transfer of substrate to CCT/TriC;Folding of actin by CCT/TriC;Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding;BBSome-mediated cargo-targeting to cilium;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance
(Consensus)
Recessive Scores
- pRec
- 0.656
Intolerance Scores
- loftool
- 0.301
- rvis_EVS
- -0.36
- rvis_percentile_EVS
- 29.16
Haploinsufficiency Scores
- pHI
- 0.359
- hipred
- Y
- hipred_score
- 0.831
- ghis
- 0.611
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.925
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tcp1
- Phenotype
Zebrafish Information Network
- Gene name
- tcp1
- Affected structure
- skeletal muscle cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- protein folding;tubulin complex assembly;binding of sperm to zona pellucida;positive regulation of telomere maintenance via telomerase;interleukin-12-mediated signaling pathway;translocation of peptides or proteins into host cell cytoplasm;protein stabilization;positive regulation of telomerase activity;scaRNA localization to Cajal body;toxin transport;positive regulation of establishment of protein localization to telomere;positive regulation of protein localization to Cajal body;positive regulation of telomerase RNA localization to Cajal body;regulation of macrophage apoptotic process
- Cellular component
- pericentriolar material;acrosomal vesicle;zona pellucida receptor complex;nuclear heterochromatin;Golgi apparatus;centrosome;cytosol;chaperonin-containing T-complex;microtubule;myelin sheath;cell body;extracellular exosome
- Molecular function
- RNA binding;protein binding;ATP binding;ubiquitin protein ligase binding;unfolded protein binding