TUBE1

protein-coding

tubulin epsilon 1, the group of Tubulins

Gene summary

This gene encodes a member of the tubulin superfamily. This protein localizes to the centriolar sub-distal appendages that are associated with the older of the two centrioles after centrosome duplication. This protein plays a central role in organization of the microtubules during centriole duplication. A pseudogene of this gene is found on chromosome 5.[provided by RefSeq, Jan 2009]

MANE transcript

NM_016262.5

Inheritance

—

ClinVar variants

U:52B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr6:112,070,663-112,087,529

External References & Databases

Ensembl (ENSG00000074935)

Transcript & Mutation Effects

hg38 • Region Span ~16.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to TUBE1 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 48

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016262.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			47 clinvar	1 clinvar		48
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	52	1	0	53

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016262.5	RefSeq	NP_057346.1	12	MANE Select
ENST00000368662.10	Ensembl	ENSP00000357651.5	12	MANE Select
ENST00000604743.5	Ensembl	ENSP00000475087.1	4	Standard
ENST00000604967.1	Ensembl	ENSP00000474989.1	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

microtubule cytoskeleton organization
mitotic cell cycle
microtubule-based process
centrosome cycle

Molecular Function

GTPase activity
structural constituent of cytoskeleton
GTP binding

Cellular Component

pericentriolar material
cytoplasm
microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368662
Coding exons: 12
Length: 16753
Individuals with no LoFs: 125692
Homozygous LoFs: 0
Heterozygous LoFs: 48
Defined: 125740
p: 0.000191

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.397	232	250	0.929	0.0000120	3135
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00029	0.00026	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00034	0.00033	rare
Finnish	0.000093	0.000092	rare
European (Non-Finnish)	0.00017	0.00017	rare
South Asian	0.00035	0.00033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.230

Intolerance Scores

LoFtool: 0.587
RVIS EVS: 0.13
RVIS percentile EVS: 63.36

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: N
Indispensability score: 0.225

Gene Damage Prediction

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