TUBGCP2

tubulin gamma complex associated protein 2, the group of Tubulin gamma complex associated protein family

Basic information

Region (hg38): 10:133278634-133318823

Links

ENSG00000130640 ∙ NCBI:10844 ∙ OMIM:617817 ∙ HGNC:18599 ∙ Uniprot:Q9BSJ2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• 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: CGD

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 ClinVar and linked to the TUBGCP2 gene.

• Inborn genetic diseases (51 variants)
• not provided (47 variants)
• Pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures (13 variants)
• not specified (4 variants)
• TUBGCP2-related condition (3 variants)
• Abnormality of neuronal migration (2 variants)

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			2	15	6	23
missense			52	4		56
nonsense						0
start loss						0
frameshift	1					1
inframe indel						0
splice donor/acceptor (+/-2bp)			3			3
splice region			2	6		8
non coding			10	3	4	17
Total	1	0	67	22	10

Highest pathogenic variant AF is 0.0000328

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	Likely benign (Mar 26, 2024)
10-133279825-C-G		not specified	Uncertain significance (Jan 31, 2022)
10-133279828-G-T		not specified	Uncertain significance (Jul 22, 2022)
10-133279872-C-T		not specified	Uncertain significance (Nov 07, 2022)
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-C		not specified	Uncertain significance (Jul 13, 2022)
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)
10-133282313-G-A		TUBGCP2-related disorder	Uncertain significance (Mar 29, 2023)
10-133282347-G-A		TUBGCP2-related disorder	Likely benign (Feb 01, 2024)
10-133282347-G-T		TUBGCP2-related disorder	Likely benign (Sep 29, 2023)
10-133283087-G-A		TUBGCP2-related disorder	Benign/Likely benign (Jun 01, 2022)
10-133283094-A-C		not specified	Uncertain significance (Dec 12, 2023)
10-133283159-G-A		TUBGCP2-related disorder	Likely benign (Jul 29, 2022)
10-133283187-G-A		not specified	Uncertain significance (Jan 26, 2022)
10-133283206-C-T		not specified	Uncertain significance (Dec 22, 2023)

GnomAD

Source: gnomAD

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: dbNSFP

• 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
• 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

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