TUBD1

tubulin delta 1, the group of Tubulins

Basic information

Region (hg38): 17:59859426-59892945

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.

• not_specified (44 variants)
• not_provided (1 variants)
• Polydactyly (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. These statistics are base on transcript: NM_000016261.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					1	1
missense			42	3		45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	42	3	1

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