TUBA1C

tubulin alpha 1c, the group of Tubulins

Basic information

Region (hg38): 12:49188736-49274600

Previous symbols: [ "TUBA6" ]

Links

ENSG00000167553 ∙ NCBI:84790 ∙ ∙ HGNC:20768 ∙ Uniprot:Q9BQE3 ∙ 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 TUBA1C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUBA1C 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				1		1
missense			13	1		14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	2	0

Variants in TUBA1C

This is a list of pathogenic ClinVar variants found in the TUBA1C region.

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

Position	Type	Phenotype	Significance	ClinVar
12-49188808-T-TGCG			Likely benign (Oct 24, 2018)
12-49188874-G-A			Likely benign (Jul 05, 2018)
12-49188909-T-G			Benign (Jun 26, 2018)
12-49188957-G-A			Likely benign (Nov 24, 2023)
12-49188968-G-T			Likely benign (Apr 24, 2018)
12-49188973-TC-T		Lissencephaly due to TUBA1A mutation	Likely pathogenic (Oct 19, 2020)
12-49228037-C-T			Likely benign (Nov 01, 2023)
12-49269480-A-G		not specified	Uncertain significance (Dec 14, 2022)
12-49269546-G-A		not specified	Uncertain significance (Apr 22, 2024)
12-49269589-G-C		not specified	Uncertain significance (Jan 30, 2024)
12-49269589-G-T		not specified	Uncertain significance (Aug 02, 2021)
12-49269950-C-T		not specified	Uncertain significance (May 09, 2023)
12-49272329-C-G		not specified	Uncertain significance (Jan 18, 2023)
12-49272511-A-C		not specified	Uncertain significance (Jan 26, 2023)
12-49272526-C-A		not specified	Uncertain significance (Jun 19, 2024)
12-49272540-C-T			Likely benign (Apr 01, 2023)
12-49272659-C-G		not specified	Uncertain significance (Jan 18, 2022)
12-49272799-C-T		not specified	Uncertain significance (Oct 03, 2022)
12-49272892-C-T		not specified	Uncertain significance (Mar 11, 2022)
12-49272895-A-G		not specified	Uncertain significance (Nov 29, 2023)
12-49272949-C-G		not specified	Uncertain significance (Aug 08, 2022)
12-49273027-G-A		not specified	Likely benign (Apr 12, 2022)
12-49273036-G-A		not specified	Uncertain significance (Nov 18, 2022)
12-49273079-A-C		not specified	Uncertain significance (Apr 23, 2024)
12-49273091-T-C		not specified	Uncertain significance (Apr 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TUBA1C	protein_coding	protein_coding	ENST00000301072	4	84596

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00743	0.978	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.17	165	264	0.624	0.0000163	2955
Missense in Polyphen		51	117.13	0.43541		1394
Synonymous	-0.708	108	99.0	1.09	0.00000581	896
Loss of Function	2.15	6	15.0	0.401	8.33e-7	172

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000272	0.000272
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000217
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.000223	0.000217
South Asian	0.00	0.00
Other	0.000339	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.
• 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;stathmin and breast cancer resistance to antimicrotubule agents;downregulated of mta-3 in er-negative breast tumors;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;Prefoldin mediated transfer of substrate to CCT/TriC;Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding;Post-chaperonin tubulin folding pathway (Consensus)

Intolerance Scores

• rvis_EVS: -0.58
• rvis_percentile_EVS: 18.44

Haploinsufficiency Scores

• pHI: 0.321
• hipred: Y
• hipred_score: 0.840
• ghis: 0.634

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.989

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tuba1c

Gene ontology

• Biological process: microtubule cytoskeleton organization;mitotic cell cycle;microtubule-based process;cytoskeleton-dependent intracellular transport;cell division
• Cellular component: nucleus;cytoplasm;microtubule;microtubule cytoskeleton;vesicle
• Molecular function: GTPase activity;structural molecule activity;structural constituent of cytoskeleton;protein binding;GTP binding