TUBG1

tubulin gamma 1, the group of Tubulins

Basic information

Region (hg38): 17:42609641-42615238

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 (Moderate), mode of inheritance: AD
complex cortical dysplasia with other brain malformations 4 (Strong), 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 (126 variants)
Complex_cortical_dysplasia_with_other_brain_malformations_4 (22 variants)
not_specified (18 variants)
Inborn_genetic_diseases (16 variants)
TUBG1-related_disorder (10 variants)
Lissencephaly (3 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. These statistics are base on transcript: NM_000001070.5. 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			1 clinvar	48 clinvar	3 clinvar	52
missense	2 clinvar	13 clinvar	42 clinvar	1 clinvar		58
nonsense			1 clinvar	1 clinvar		2
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)		1 clinvar	2 clinvar			3
Total	2	14	48	50	3

Highest pathogenic variant AF is 6.8456484e-7

Loading clinvar variants...

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