VPS9D1

Chr 16

VPS9 domain containing 1

Also known as: ATP-BL, ATPBL, C16orf7

NCBI Gene: 9605ENSG00000075399UniProt: Q9Y2B5

Enables identical protein binding activity. Predicted to be involved in proton motive force-driven ATP synthesis. Predicted to be active in cytosol and endocytic vesicle. [provided by Alliance of Genome Resources, Jul 2025]

0
Active trials
41
Pathogenic / LP
210
ClinVar variants
6
Pubs (1 yr)
-0.2
Missense Z
1.31
LOEUF
Clinical Summary— VPS9D1
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
41 Pathogenic / Likely Pathogenic· 162 VUS of 210 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
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.
1.31LOEUF
pLI 0.000
Z-score 0.17
OE 0.97 (0.72–1.31)
Tolerant

Highly tolerant — LoF variants common in population

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.
-0.15Z-score
OE missense 1.02 (0.94–1.11)
364 obs / 356.0 exp
Tolerant

Tolerant to missense variation

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.0.97 (0.72–1.31)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.1.02 (0.94–1.11)
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.1.17
0≤1.21.6
LoF obs/exp: 30 / 31.0Missense obs/exp: 364 / 356.0Syn Z: -1.78

ClinVar Variant Classifications

210 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic34
Likely Pathogenic7
VUS162
Likely Benign5
Benign2
34
Pathogenic
7
Likely Pathogenic
162
VUS
5
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
34
0
34
Likely Pathogenic
0
0
7
0
7
VUS
0
133
29
0
162
Likely Benign
0
3
1
1
5
Benign
0
0
0
2
2
Total0136713210

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

VPS9D1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Landmark / reviewRecent case evidence
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
VPS9D1-AS1 antisense therapy via lipid nanoparticles reprograms cold tumors and enhances immunotherapy in colorectal cancer.
Yang L et al.·J Control Release
2025
Decreased expression of lncRNA VPS9D1-AS1 in gastric cancer and its clinical significance.
Chen M et al.·Cancer Biomark
2017
Long non-coding RNA VPS9D1-AS1 enhances proliferation, invasion, and epithelial-mesenchymal transition in endometrial cancer via miR-377-3p/SGK1.
Peng TF et al.·Kaohsiung J Med Sci
2022
Long noncoding RNA VPS9D1-AS1 augments the malignant phenotype of non-small cell lung cancer by sponging microRNA-532-3p and thereby enhancing HMGA2 expression.
Han X et al.·Aging (Albany NY)
2020
VPS9D1-AS1 gene rs7206570 polymorphism associated with the clinical stage of colorectal cancer and binding with hsa-miR-361-3p.
Gao X et al.·Hum Cell
2022
Top 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Emergence and Tandem Repeat-Mediated Elongation of a Translated De Novo Open Reading Frame in Human Oncogenic RNA Gene VPS9D1-AS1 (MYU).
Chou L et al.·Genome Biol Evol
2026Open Access
VPS9D1-AS1: a critical oncogenic long non-coding RNA in human malignancies.
Wang B et al.·Clin Transl Oncol
2025
Exosomal transfer of VPS9D1-AS1 induces M2 polarization to promote erlotinib resistance of LUAD cells via activation of the Wnt/β-catenin signaling pathway.
Teng Z et al.·Biochem Pharmacol
2026
Long Non-Coding RNA VPS9D1-AS1 in Human Cancer: Functions, Mechanisms, and Clinical Utility.
Yang J et al.·Anticancer Agents Med Chem
2025Functional
Plasma expression of antisense LncRNAs RBM5-AS1, VPS9D1-AS1 and STEAP3-AS1 as novel biomarkers for colorectal cancer diagnosis.
Karbalaei Hashemiyan M et al.·Mol Biol Rep
2025
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients