TUBA3E

tubulin alpha 3e, the group of Tubulins

Basic information

Region (hg38): 2:130191744-130198439

Links

ENSG00000152086 ∙ NCBI:112714 ∙ OMIM:619918 ∙ HGNC:20765 ∙ Uniprot:Q6PEY2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the TUBA3E gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUBA3E 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				3	2	5
missense			25	3	4	32
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region				1		1
non coding					1	1
Total	0	0	26	6	7

Variants in TUBA3E

This is a list of pathogenic ClinVar variants found in the TUBA3E region.

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

Position	Type	Phenotype	Significance	ClinVar
2-130191842-C-T		not specified	Uncertain significance (Jul 14, 2022)
2-130191892-T-C		not specified	Uncertain significance (Sep 16, 2021)
2-130191907-G-T		Neurodevelopmental disorder	Uncertain significance (Mar 12, 2024)
2-130191918-G-A			Benign (Jan 12, 2018)
2-130191938-C-T			Likely benign (May 01, 2023)
2-130191967-T-C		not specified	Uncertain significance (Mar 03, 2022)
2-130192009-A-T		not specified	Likely benign (Apr 12, 2022)
2-130192029-C-T			Likely benign (Apr 01, 2024)
2-130192039-G-A		not specified	Uncertain significance (Mar 19, 2024)
2-130193785-C-T			Uncertain significance (Dec 30, 2021)
2-130193799-G-A		not specified	Uncertain significance (May 09, 2022)
2-130193915-A-G			Likely benign (Sep 28, 2017)
2-130193958-C-G		not specified	Uncertain significance (Jan 19, 2024)
2-130194039-G-C		not specified	Uncertain significance (Jan 04, 2022)
2-130194046-G-T		not specified	Uncertain significance (May 22, 2023)
2-130194054-G-T		not specified	Uncertain significance (Jul 15, 2021)
2-130194064-C-T		not specified	Uncertain significance (Aug 12, 2021)
2-130194156-C-T		not specified	Uncertain significance (Apr 15, 2022)
2-130194157-G-A		not specified	Uncertain significance (Jun 29, 2022)
2-130194169-T-C		not specified	Uncertain significance (Jan 22, 2024)
2-130194171-T-G		not specified	Uncertain significance (May 23, 2023)
2-130194173-C-T			Likely benign (Mar 01, 2022)
2-130194181-G-T			Benign (Feb 13, 2020)
2-130194195-T-C		not specified	Uncertain significance (Aug 16, 2022)
2-130194199-G-A		Seizure;Primary microcephaly;Lissencephaly;Global developmental delay	Likely pathogenic (Dec 01, 2014)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TUBA3E	protein_coding	protein_coding	ENST00000312988	5	6717

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.03e-8	0.258	125019	7	722	125748	0.00290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.296	299	285	1.05	0.0000181	2921
Missense in Polyphen		160	145.1	1.1027		1495
Synonymous	0.144	117	119	0.983	0.00000812	892
Loss of Function	0.509	13	15.1	0.859	7.34e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0380	0.0382
Ashkenazi Jewish	0.00	0.00
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000483	0.000475
Middle Eastern	0.000218	0.000217
South Asian	0.000850	0.000850
Other	0.000979	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Tubulin is the major constituent of microtubules. It binds two moles of GTP, one at an exchangeable site on the beta chain and one at a non-exchangeable site on the alpha chain (By similarity). {ECO:0000250}.
• Pathway: Tight junction - Homo sapiens (human);Phagosome - Homo sapiens (human);Gap junction - Homo sapiens (human);Pathogenic Escherichia coli infection - Homo sapiens (human);Apoptosis - Homo sapiens (human);Pathogenic Escherichia coli infection;Parkin-Ubiquitin Proteasomal System pathway;Post-translational protein modification;Metabolism of proteins;Chaperonin-mediated protein folding;Formation of tubulin folding intermediates by CCT/TriC;Carboxyterminal post-translational modifications of tubulin;Protein folding;Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding;Post-chaperonin tubulin folding pathway (Consensus)

Recessive Scores

• pRec: 0.172

Intolerance Scores

• loftool: 0.527
• rvis_EVS: 0.38
• rvis_percentile_EVS: 75.58

Haploinsufficiency Scores

• pHI: 0.514
• hipred: N
• hipred_score: 0.396
• ghis: 0.392

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tuba3b

Gene ontology

• Biological process: microtubule cytoskeleton organization;mitotic cell cycle;microtubule-based process;biological_process
• Cellular component: nucleus;cytoplasm;microtubule;microtubule cytoskeleton
• Molecular function: molecular_function;GTPase activity;structural constituent of cytoskeleton;protein binding;GTP binding