TUBG1

tubulin gamma 1, the group of Tubulins

Basic information

Region (hg38): 17:42609640-42615238

Previous symbols: [ "TUBG" ]

Links

ENSG00000131462 ∙ NCBI:7283 ∙ OMIM:191135 ∙ HGNC:12417 ∙ Uniprot:P23258 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex cortical dysplasia with other brain malformations 4 (Strong), mode of inheritance: AD
• complex cortical dysplasia with other brain malformations 4 (Moderate), mode of inheritance: AD
• lissencephaly spectrum disorders (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cortical dysplasia, complex, with other brain malformations 4	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	23603762

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TUBG1 gene.

• not provided (96 variants)
• not specified (15 variants)
• Complex cortical dysplasia with other brain malformations 4 (12 variants)
• Inborn genetic diseases (2 variants)
• Lissencephaly (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUBG1 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			1	31	4	36
missense	1	6	15	1		23
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			7	5	1	13
non coding			2	22	10	34
Total	1	6	20	54	14

Variants in TUBG1

This is a list of pathogenic ClinVar variants found in the TUBG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-42609680-G-T			Likely benign (Jul 06, 2018)
17-42609689-C-A		not specified	Likely benign (Jul 11, 2017)
17-42609722-C-T		not specified	Likely benign (Jun 26, 2017)
17-42609732-G-A			Benign (Dec 30, 2019)
17-42609733-G-A			Uncertain significance (Sep 01, 2016)
17-42609743-G-A			Likely benign (Mar 30, 2018)
17-42609766-T-A		Inborn genetic diseases	Uncertain significance (Feb 09, 2022)
17-42609789-G-A			Uncertain significance (Sep 10, 2023)
17-42609800-C-T			Likely benign (Jun 30, 2022)
17-42609804-C-G			Benign (Aug 20, 2023)
17-42609806-C-T			Likely benign (Nov 18, 2022)
17-42610089-G-A			Likely benign (Jun 07, 2022)
17-42610093-G-T			Benign/Likely benign (Jul 26, 2023)
17-42610102-C-T		Inborn genetic diseases	Uncertain significance (Nov 01, 2021)
17-42610105-C-A			Uncertain significance (Dec 19, 2021)
17-42610105-C-G			Uncertain significance (Jan 05, 2022)
17-42610106-A-T			Uncertain significance (Jan 19, 2023)
17-42610111-G-A			Uncertain significance (Feb 27, 2023)
17-42610175-G-A			Likely benign (Jul 21, 2023)
17-42610184-C-T			Likely benign (May 14, 2018)
17-42610208-C-T		TUBG1-related disorder	Likely benign (Aug 29, 2022)
17-42610238-GC-G			Likely benign (Jun 29, 2022)
17-42610239-C-T		not specified	Likely benign (May 19, 2022)
17-42610407-G-T			Likely benign (Dec 11, 2023)
17-42610412-C-T			Likely benign (May 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TUBG1	protein_coding	protein_coding	ENST00000251413	11	5559

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.129	0.871	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	4.16	82	276	0.297	0.0000168	2966
Missense in Polyphen		23	107.15	0.21465		1234
Synonymous	0.0702	110	111	0.992	0.00000666	868
Loss of Function	3.27	6	22.9	0.262	0.00000107	255

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.000896	0.000893
East Asian	0.000109	0.000109
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.000163	0.000163
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tubulin is the major constituent of microtubules. The gamma chain is found at microtubule organizing centers (MTOC) such as the spindle poles or the centrosome. Pericentriolar matrix component that regulates alpha/beta chain minus-end nucleation, centrosome duplication and spindle formation.
• Disease: DISEASE: Cortical dysplasia, complex, with other brain malformations 4 (CDCBM4) [MIM:615412]: A disorder of aberrant neuronal migration and disturbed axonal guidance. Clinical features include early-onset seizures, microcephaly, spastic tetraplegia, and various malformations of cortical development, such as agyria, posterior or frontal pachygyria, thick cortex, and subcortical band heterotopia and thin corpus callosum in some patients. {ECO:0000269|PubMed:23603762}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Human papillomavirus infection - Homo sapiens (human);Regulation of PLK1 Activity at G2/M Transition;Recruitment of mitotic centrosome proteins and complexes;Loss of Nlp from mitotic centrosomes;Loss of proteins required for interphase microtubule organization from the centrosome;Centrosome maturation;AURKA Activation by TPX2;G2/M Transition;Mitotic G2-G2/M phases;Recruitment of NuMA to mitotic centrosomes;Mitotic Prometaphase;M Phase;Cell Cycle;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;PLK1 signaling events;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.493

Intolerance Scores

• loftool: 0.379
• rvis_EVS: -0.16
• rvis_percentile_EVS: 41.64

Haploinsufficiency Scores

• pHI: 0.647
• hipred: Y
• hipred_score: 0.771
• ghis: 0.589

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.644

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tubg1
• Phenotype: cellular phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype

Zebrafish Information Network

• Gene name: tubg1
• Affected structure: hepatocyte
• Phenotype tag: abnormal
• Phenotype quality: increased size

Gene ontology

• Biological process: mitotic sister chromatid segregation;G2/M transition of mitotic cell cycle;meiotic spindle organization;microtubule cytoskeleton organization;mitotic cell cycle;microtubule-based process;microtubule nucleation;mitotic spindle organization;regulation of G2/M transition of mitotic cell cycle;cytoplasmic microtubule organization;ciliary basal body-plasma membrane docking
• Cellular component: pericentriolar material;condensed nuclear chromosome;gamma-tubulin complex;nucleus;cytoplasm;centrosome;centriole;spindle;polar microtubule;cytosol;microtubule;cytoplasmic microtubule;cell leading edge;ciliary basal body;apical part of cell;recycling endosome;non-motile cilium
• Molecular function: GTPase activity;structural constituent of cytoskeleton;protein binding;GTP binding;identical protein binding