TUBE1

tubulin epsilon 1, the group of Tubulins

Basic information

Region (hg38): 6:112070663-112087529

Links

ENSG00000074935 ∙ NCBI:51175 ∙ OMIM:607345 ∙ HGNC:20775 ∙ Uniprot:Q9UJT0 ∙ 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 TUBE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUBE1 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			17			17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	0	0

Variants in TUBE1

This is a list of pathogenic ClinVar variants found in the TUBE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-112071447-C-T		not specified	Uncertain significance (Jan 09, 2024)
6-112071450-G-T		not specified	Uncertain significance (Jul 09, 2021)
6-112071453-T-C		not specified	Uncertain significance (May 08, 2024)
6-112071489-T-C		not specified	Uncertain significance (Oct 05, 2023)
6-112071519-T-C		not specified	Uncertain significance (Oct 27, 2022)
6-112071537-T-C		not specified	Uncertain significance (Feb 06, 2024)
6-112071540-C-T		not specified	Uncertain significance (Jun 28, 2022)
6-112071554-T-C		not specified	Uncertain significance (Jun 13, 2024)
6-112072849-G-A		not specified	Uncertain significance (Sep 13, 2023)
6-112074734-G-A		not specified	Uncertain significance (Dec 28, 2023)
6-112074765-C-T		not specified	Uncertain significance (Dec 27, 2023)
6-112075973-T-C		not specified	Uncertain significance (Aug 17, 2022)
6-112076040-T-C		not specified	Uncertain significance (May 31, 2023)
6-112076042-G-A		not specified	Uncertain significance (Jun 19, 2024)
6-112076447-A-C		not specified	Uncertain significance (Dec 16, 2022)
6-112079638-C-T		not specified	Uncertain significance (Dec 30, 2023)
6-112084206-A-G		not specified	Uncertain significance (Nov 09, 2021)
6-112084207-T-C		not specified	Uncertain significance (Sep 17, 2021)
6-112086583-C-G		not specified	Uncertain significance (Jan 23, 2024)
6-112087422-C-T		not specified	Uncertain significance (Apr 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TUBE1	protein_coding	protein_coding	ENST00000368662	12	16753

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0269	0.973	125692	0	48	125740	0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.397	232	250	0.929	0.0000120	3135
Missense in Polyphen		79	83.289	0.94851		1113
Synonymous	1.09	77	90.1	0.854	0.00000472	872
Loss of Function	3.07	7	22.8	0.307	0.00000106	306

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000410	0.000410
Ashkenazi Jewish	0.00	0.00
East Asian	0.000338	0.000326
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000170	0.000167
Middle Eastern	0.000338	0.000326
South Asian	0.000347	0.000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.230

Intolerance Scores

• loftool: 0.587
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.36

Haploinsufficiency Scores

• pHI: 0.133
• hipred: N
• hipred_score: 0.204
• ghis: 0.548

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.225

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tube1

Gene ontology

• Biological process: microtubule cytoskeleton organization;mitotic cell cycle;microtubule-based process;centrosome cycle
• Cellular component: pericentriolar material;cytoplasm;microtubule
• Molecular function: GTPase activity;structural constituent of cytoskeleton;GTP binding