TUBAL3

tubulin alpha like 3, the group of Tubulins

Basic information

Region (hg38): 10:5393101-5404828

Links

ENSG00000178462 ∙ NCBI:79861 ∙ ∙ HGNC:23534 ∙ Uniprot:A6NHL2 ∙ 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 TUBAL3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUBAL3 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			35	4	1	40
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	35	7	3

Variants in TUBAL3

This is a list of pathogenic ClinVar variants found in the TUBAL3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-5393521-A-T		not specified	Uncertain significance (Feb 12, 2024)
10-5393537-C-G		not specified	Uncertain significance (May 03, 2023)
10-5393539-T-A		not specified	Uncertain significance (May 03, 2023)
10-5393540-C-T		not specified	Uncertain significance (Apr 16, 2024)
10-5393620-T-C		not specified	Uncertain significance (Jun 06, 2023)
10-5393640-G-A		not specified	Likely benign (Dec 08, 2023)
10-5393692-G-A		not specified	Uncertain significance (Dec 02, 2022)
10-5393753-C-T		not specified	Uncertain significance (Aug 13, 2021)
10-5393778-C-T			Likely benign (Mar 01, 2023)
10-5393782-T-G		not specified	Uncertain significance (Aug 01, 2023)
10-5393822-G-A		not specified	Uncertain significance (May 25, 2022)
10-5393827-G-A		not specified	Uncertain significance (Jan 02, 2024)
10-5393840-C-T		not specified	Uncertain significance (Nov 08, 2022)
10-5393841-G-A			Benign (Jul 23, 2018)
10-5393914-C-T		not specified	Uncertain significance (Dec 27, 2023)
10-5393952-G-C		not specified	Uncertain significance (Mar 19, 2024)
10-5393974-A-T		not specified	Uncertain significance (May 23, 2024)
10-5393982-C-G		not specified	Uncertain significance (Sep 01, 2021)
10-5394014-T-C		not specified	Uncertain significance (Jan 23, 2023)
10-5394020-C-T			Uncertain significance (May 01, 2019)
10-5394031-A-T		not specified	Uncertain significance (Oct 03, 2022)
10-5394046-C-A		not specified	Uncertain significance (Dec 14, 2023)
10-5394056-G-T		not specified	Uncertain significance (Jan 09, 2024)
10-5394134-C-T			Likely benign (Mar 01, 2023)
10-5394185-C-T		not specified	Uncertain significance (Jan 25, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TUBAL3	protein_coding	protein_coding	ENST00000380419	4	11733

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.44e-8	0.283	125678	0	70	125748	0.000278

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.318	283	268	1.05	0.0000159	2917
Missense in Polyphen		117	108	1.0834		1280
Synonymous	-0.0666	108	107	1.01	0.00000684	896
Loss of Function	0.483	12	13.9	0.860	7.59e-7	164

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00109	0.00108
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000360	0.000352
Middle Eastern	0.000217	0.000217
South Asian	0.0000981	0.0000980
Other	0.000163	0.000163

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;Metabolism of proteins;Chaperonin-mediated protein folding;Formation of tubulin folding intermediates by CCT/TriC;Protein folding;Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding;Post-chaperonin tubulin folding pathway (Consensus)

Recessive Scores

• pRec: 0.154

Intolerance Scores

• loftool: 0.141
• rvis_EVS: -0.57
• rvis_percentile_EVS: 18.96

Haploinsufficiency Scores

• pHI: 0.0537
• hipred: N
• hipred_score: 0.439
• ghis: 0.404

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.129

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tubal3

Gene ontology

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