TUBGCP3

tubulin gamma complex associated protein 3, the group of Tubulin gamma complex associated protein family

Basic information

Region (hg38): 13:112485011-112588205

Links

ENSG00000126216 ∙ NCBI:10426 ∙ OMIM:617818 ∙ HGNC:18598 ∙ Uniprot:Q96CW5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TUBGCP3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUBGCP3 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						0
missense			35	1		36
nonsense						0
start loss						0
frameshift						0
inframe indel				1	1	2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	2	1

Variants in TUBGCP3

This is a list of pathogenic ClinVar variants found in the TUBGCP3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
13-112486096-C-T		not specified	Uncertain significance (Dec 06, 2023)
13-112499113-T-C		not specified	Uncertain significance (Dec 17, 2023)
13-112504058-G-A		not specified	Uncertain significance (Nov 08, 2022)
13-112504061-A-G		not specified	Uncertain significance (Feb 06, 2023)
13-112504086-G-T		not specified	Uncertain significance (May 25, 2023)
13-112516488-T-C		not specified	Uncertain significance (Oct 13, 2023)
13-112516494-T-C		not specified	Uncertain significance (Feb 12, 2024)
13-112516502-T-C		not specified	Uncertain significance (Aug 01, 2022)
13-112519016-C-A		not specified	Uncertain significance (Mar 25, 2024)
13-112519890-A-G		not specified	Uncertain significance (Aug 10, 2021)
13-112527387-T-C		not specified	Uncertain significance (Apr 19, 2024)
13-112545739-C-T		not specified	Uncertain significance (Jan 16, 2024)
13-112545808-G-A		not specified	Uncertain significance (Dec 07, 2023)
13-112545809-G-A		not specified	Uncertain significance (Dec 22, 2023)
13-112545838-G-A		not specified	Uncertain significance (Sep 27, 2021)
13-112547517-ACGCGCGTGGGAAAGACGTGCATGGGAAAGT-A			Likely benign (May 01, 2023)
13-112547538-ATGGGAAAGTCGCGCG-A		not specified	Benign (Dec 12, 2023)
13-112547673-T-C		not specified	Uncertain significance (Apr 25, 2023)
13-112547691-C-T		not specified	Uncertain significance (May 26, 2023)
13-112548133-C-T		not specified	Uncertain significance (Dec 20, 2021)
13-112554065-C-T		not specified	Uncertain significance (Nov 22, 2022)
13-112554080-G-A		not specified	Uncertain significance (Apr 05, 2023)
13-112554900-T-C		not specified	Uncertain significance (Mar 20, 2024)
13-112554946-T-C		not specified	Uncertain significance (Apr 18, 2024)
13-112554958-C-T		not specified	Uncertain significance (Nov 21, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TUBGCP3	protein_coding	protein_coding	ENST00000261965	22	103157

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.455	0.545	125711	0	37	125748	0.000147

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.52	353	513	0.688	0.0000294	5932
Missense in Polyphen		38	97.057	0.39152		1198
Synonymous	0.765	180	194	0.930	0.0000113	1728
Loss of Function	5.50	13	58.4	0.223	0.00000348	622

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000209	0.000206
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000946	0.0000924
European (Non-Finnish)	0.000186	0.000185
Middle Eastern	0.0000544	0.0000544
South Asian	0.000164	0.000163
Other	0.000164	0.000163

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: 0.135

Intolerance Scores

• rvis_EVS: -1.51
• rvis_percentile_EVS: 3.5

Haploinsufficiency Scores

• pHI: 0.551
• hipred: Y
• hipred_score: 0.800
• ghis: 0.676

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.829

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Tubgcp3

Gene ontology

• Biological process: mitotic cell cycle;microtubule nucleation;single fertilization;cytoplasmic microtubule organization;spindle assembly;meiotic cell cycle;microtubule nucleation by interphase microtubule organizing center
• Cellular component: equatorial microtubule organizing center;gamma-tubulin complex;cytoplasm;centrosome;centriole;spindle;polar microtubule;cytosol;gamma-tubulin small complex;membrane
• Molecular function: structural molecule activity;structural constituent of cytoskeleton;protein binding;gamma-tubulin binding;microtubule minus-end binding