TUBD1

tubulin delta 1, the group of Tubulins

Basic information

Region (hg38): 17:59859478-59892945

Links

ENSG00000108423 ∙ NCBI:51174 ∙ OMIM:607344 ∙ HGNC:16811 ∙ Uniprot:Q9UJT1 ∙ 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 TUBD1 gene.

• Inborn genetic diseases (17 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the TUBD1 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			16	1		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	16	1	1

Variants in TUBD1

This is a list of pathogenic ClinVar variants found in the TUBD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-59860333-A-T		not specified	Uncertain significance (Jan 07, 2022)
17-59860407-T-C		not specified	Uncertain significance (Feb 10, 2023)
17-59860424-T-G		not specified	Uncertain significance (Jul 09, 2021)
17-59863805-G-A		not specified	Uncertain significance (Jan 04, 2022)
17-59866638-C-T		not specified	Uncertain significance (Jan 23, 2024)
17-59866705-G-A		not specified	Uncertain significance (Mar 20, 2023)
17-59866711-G-A		not specified	Uncertain significance (Apr 26, 2023)
17-59874571-T-C		not specified	Uncertain significance (Aug 01, 2022)
17-59878114-C-T		not specified	Uncertain significance (Mar 13, 2023)
17-59878139-C-A		not specified	Uncertain significance (May 09, 2023)
17-59878174-T-A		not specified	Uncertain significance (Jul 06, 2021)
17-59878241-T-C		not specified	Uncertain significance (Oct 04, 2022)
17-59878268-G-A		not specified	Uncertain significance (Oct 11, 2021)
17-59880923-G-C		not specified	Uncertain significance (Sep 20, 2023)
17-59881060-C-T		not specified	Likely benign (Apr 18, 2023)
17-59881082-C-T		not specified	Uncertain significance (Mar 06, 2023)
17-59881090-C-T		not specified	Likely benign (Sep 28, 2023)
17-59881094-G-A		not specified	Uncertain significance (May 04, 2023)
17-59886119-C-T		not specified	Uncertain significance (Sep 06, 2022)
17-59886123-A-G		Polydactyly	Uncertain significance (Mar 12, 2024)
17-59886225-T-C		not specified	Likely benign (Nov 21, 2023)
17-59890841-C-G		not specified	Uncertain significance (Nov 06, 2023)
17-59890847-A-G			Benign (Jul 05, 2018)
17-59890897-T-C		not specified	Uncertain significance (Aug 02, 2022)
17-59890897-T-G		not specified	Uncertain significance (Feb 27, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
TUBD1	protein_coding	protein_coding	ENST00000325752	8	33454

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000115	0.946	125682	0	63	125745	0.000251

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.535	216	239	0.903	0.0000117	3014
Missense in Polyphen		52	64.303	0.80868		788
Synonymous	0.273	78	81.1	0.961	0.00000400	808
Loss of Function	1.85	13	22.5	0.579	0.00000113	273

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000881	0.000880
Ashkenazi Jewish	0.00	0.00
East Asian	0.000332	0.000326
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000292	0.000290
Middle Eastern	0.000332	0.000326
South Asian	0.0000327	0.0000327
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a positive regulator of hedgehog signaling and regulates ciliary function. {ECO:0000250|UniProtKB:Q9R1K7}.

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.754
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.289
• ghis: 0.511

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.537

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Tubd1

Gene ontology

• Biological process: microtubule cytoskeleton organization;mitotic cell cycle;microtubule-based process;multicellular organism development;cell projection organization;positive regulation of smoothened signaling pathway
• Cellular component: nucleoplasm;cytoplasm;centriole;cytosol;microtubule;cilium
• Molecular function: GTPase activity;structural constituent of cytoskeleton;GTP binding