TUBD1
Chr 17tubulin delta 1
Also known as: TUBD
Predicted to enable GTP binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in microtubule cytoskeleton organization; mitotic cell cycle; and positive regulation of smoothened signaling pathway. Located in cytosol and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
Clinical Summary— TUBD1
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Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
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ClinVar Variants
13 Pathogenic / Likely Pathogenic· 48 VUS of 65 total submissions
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Tolerant — LoF & missense variants common in population
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.92LOEUF
pLI 0.000
Z-score 1.85
OE 0.58 (0.38–0.92)
Typical tolerance to LoF variation
Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.53Z-score
OE missense 0.90 (0.81–1.01)
216 obs / 239.3 exp
Mild missense constraint
Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.58 (0.38–0.92)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.90 (0.81–1.01)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.96
0≤1.21.6
LoF obs/exp: 13 / 22.5Missense obs/exp: 216 / 239.3Syn Z: 0.27
ClinVar Variant Classifications
65 submitted variants in ClinVar
Classification Summary
Pathogenic11
Likely Pathogenic2
VUS48
Likely Benign3
Benign1
11
Pathogenic
2
Likely Pathogenic
48
VUS
3
Likely Benign
1
Benign
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 11 | 0 | 11 |
Likely Pathogenic | 0 | 0 | 2 | 0 | 2 |
VUS | 0 | 46 | 2 | 0 | 48 |
Likely Benign | 0 | 3 | 0 | 0 | 3 |
Benign | 0 | 0 | 0 | 1 | 1 |
| Total | 0 | 49 | 15 | 1 | 65 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
TUBD1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
OMIM — Genotype-Phenotype Relationships
1 OMIM entry
TUBULIN, DELTA-1; TUBD1
MIM #607344 · *
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
Genome-wide mRNA analysis reveals a TUBD1 isoform profile as a potential biomarker for diabetic retinopathy development.
Villegas-Ruiz V et al.·Exp Eye Res
2017
A Genome-Wide Association Study of Metabolic Syndrome in the Taiwanese Population.
Ho CY et al.·Nutrients
2023
Identification of Anticancer Targets in Ovarian Cancer Using Genomic Drug Sensitivity Data.
Son Y et al.·Int J Mol Sci
2025
Large-Scale Exome-wide Association Analysis Identifies Loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases.
Tajuddin SM et al.·Am J Hum Genet
2016Meta-analysis
Top 4 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Circular RNA TUBD1 Acts as the miR-146a-5p Sponge to Affect the Viability and Pro-Inflammatory Cytokine Production of LX-2 Cells through the TLR4 Pathway.
Niu H et al.·Radiat Res
2020
A missense mutation in TUBD1 is associated with high juvenile mortality in Braunvieh and Fleckvieh cattle.
Schwarzenbacher H et al.·BMC Genomics
2016Open Access
Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
Delta tubulin stabilizes male meiotic kinetochores and aids microtubule remodeling and fertility.
Stathatos GG et al.·J Cell Biol
2025Functional
Functional analysis of a panel of molecular markers for diagnosis of systemic lupus erythematosus in rats
Azzam MA et al.·Biosci Rep
2024Functional
Per1/Per2 Disruption Reduces Testosterone Synthesis and Impairs Fertility in Elderly Male Mice
Liu Q et al.·Int J Mol Sci
2022
Effects of in vitro cytochalasin D and hypoxia on mitochondrial energetics and biogenesis, cell signal status and actin/tubulin/Hsp/MMP entity in air-breathing fish heart.
Rekha S et al.·Comp Biochem Physiol C Toxicol Pharmacol
2025
Mining massive genomic data of two Swiss Braunvieh cattle populations reveals six novel candidate variants that impair reproductive success
Häfliger IM et al.·Genet Sel Evol
2021
CircTUBD1 Regulates Radiation-induced Liver Fibrosis Response via a circTUBD1/micro-203a-3p/Smad3 Positive Feedback Loop
Niu H et al.·J Clin Transl Hepatol
2022
CircTUBD1: A Novel Circular RNA Molecule as a Therapeutic Target in Radiation-induced Liver Fibrosis
Gu CY et al.·J Clin Transl Hepatol
2022
Epsilon tubulin is an essential determinant of microtubule-based structures in male germ cells
Stathatos GG et al.·EMBO Rep
2024
Top 8 full-text resultsSearch PubTator3 ↗
External Resources
Links to major genomics databases and tools