TUBGCP2
Basic information
Region (hg38): 10:133278635-133318823
Links
Phenotypes
GenCC
Source:
- Norman-Roberts syndrome (Strong), mode of inheritance: AR
- pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures (Limited), mode of inheritance: AR
- pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Cortical dysplasia, complex, with other brain malformations 15 | AR | 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 | Craniofacial; Neurologic; Ophthalmologic | 31630790 |
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUBGCP2 gene is commonly pathogenic or not.
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.
Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
---|---|---|---|---|---|---|
synonymous | 23 | 31 | ||||
missense | 89 | 97 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 3 | |||||
splice region | 2 | 8 | 10 | |||
non coding | 19 | 29 | ||||
Total | 0 | 0 | 113 | 36 | 11 |
Variants in TUBGCP2
This is a list of pathogenic ClinVar variants found in the TUBGCP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
10-133279774-C-T | not specified | Uncertain significance (Dec 19, 2022) | ||
10-133279775-G-A | TUBGCP2-related disorder | Likely benign (Sep 27, 2022) | ||
10-133279790-G-A | TUBGCP2-related disorder | Likely benign (Feb 04, 2023) | ||
10-133279803-G-A | Pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures • not specified | Conflicting classifications of pathogenicity (May 07, 2024) | ||
10-133279825-C-G | not specified | Uncertain significance (Jan 31, 2022) | ||
10-133279828-G-T | not specified | Uncertain significance (Jul 22, 2022) | ||
10-133279833-G-A | not specified | Uncertain significance (Jul 15, 2024) | ||
10-133279863-C-T | not specified | Uncertain significance (Nov 14, 2024) | ||
10-133279872-C-T | not specified | Uncertain significance (Nov 21, 2024) | ||
10-133279890-T-C | not specified | Uncertain significance (Sep 14, 2022) | ||
10-133281283-C-T | not specified | Uncertain significance (Jan 04, 2024) | ||
10-133281331-G-A | Uncertain significance (Jun 01, 2022) | |||
10-133281368-G-T | not specified | Uncertain significance (Oct 03, 2022) | ||
10-133281391-C-T | not specified | Uncertain significance (Oct 12, 2021) | ||
10-133281392-G-A | Likely benign (Jul 01, 2024) | |||
10-133281392-G-C | not specified | Uncertain significance (Jul 13, 2022) | ||
10-133281415-T-C | not specified | Likely benign (Oct 25, 2024) | ||
10-133281420-G-A | not specified | Likely benign (Mar 31, 2024) | ||
10-133282231-C-T | not specified | Likely benign (Sep 20, 2023) | ||
10-133282246-C-T | Likely benign (Sep 01, 2023) | |||
10-133282255-C-T | not specified | Uncertain significance (Mar 06, 2023) | ||
10-133282258-C-A | not specified | Uncertain significance (Dec 22, 2023) | ||
10-133282260-C-T | not specified | Likely benign (Nov 14, 2024) | ||
10-133282279-C-T | not specified | Uncertain significance (Jun 26, 2024) | ||
10-133282313-G-A | TUBGCP2-related disorder | Uncertain significance (Mar 29, 2023) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
TUBGCP2 | protein_coding | protein_coding | ENST00000543663 | 18 | 32707 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
2.20e-8 | 1.00 | 125685 | 0 | 63 | 125748 | 0.000251 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 1.24 | 491 | 575 | 0.854 | 0.0000370 | 6081 |
Missense in Polyphen | 151 | 187.6 | 0.80491 | 2043 | ||
Synonymous | -0.942 | 283 | 264 | 1.07 | 0.0000197 | 1827 |
Loss of Function | 3.21 | 20 | 42.6 | 0.470 | 0.00000207 | 489 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000293 | 0.000293 |
Ashkenazi Jewish | 0.000200 | 0.000198 |
East Asian | 0.000218 | 0.000217 |
Finnish | 0.0000462 | 0.0000462 |
European (Non-Finnish) | 0.000345 | 0.000343 |
Middle Eastern | 0.000218 | 0.000217 |
South Asian | 0.000164 | 0.000163 |
Other | 0.000490 | 0.000489 |
dbNSFP
Source:
- Function
- FUNCTION: Gamma-tubulin complex is necessary for microtubule nucleation at the centrosome.;
- Pathway
- Recruitment of mitotic centrosome proteins and complexes;Centrosome maturation;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic
(Consensus)
Recessive Scores
- pRec
- 0.274
Intolerance Scores
- loftool
- 0.721
- rvis_EVS
- -0.88
- rvis_percentile_EVS
- 10.58
Haploinsufficiency Scores
- pHI
- 0.0837
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.595
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.907
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tubgcp2
- Phenotype
Gene ontology
- Biological process
- mitotic cell cycle;microtubule nucleation;cytoplasmic microtubule organization;spindle assembly;meiotic cell cycle;microtubule nucleation by interphase microtubule organizing center;protein-containing complex assembly
- Cellular component
- spindle pole;equatorial microtubule organizing center;gamma-tubulin complex;nucleoplasm;centrosome;microtubule organizing center;cytosol;cytoplasmic microtubule;gamma-tubulin small complex;membrane
- Molecular function
- protein binding;gamma-tubulin binding;microtubule minus-end binding