PDSS2

Chr 6AR

decaprenyl diphosphate synthase subunit 2

Also known as: C6orf210, COQ10D3, COQ1B, DLP1, bA59I9.3, hDLP1

NCBI Gene: 57107ENSG00000164494UniProt: Q86YH6

The protein encoded by this gene is an enzyme that synthesizes the prenyl side-chain of coenzyme Q, or ubiquinone, one of the key elements in the respiratory chain. The gene product catalyzes the formation of all trans-polyprenyl pyrophosphates from isopentyl diphosphate in the assembly of polyisoprenoid side chains, the first step in coenzyme Q biosynthesis. Defects in this gene are a cause of coenzyme Q10 deficiency.[provided by RefSeq, Oct 2009]

Primary Disease Associations & Inheritance

Coenzyme Q10 deficiency, primary, 3MIM #614652
AR
312
ClinVar variants
26
Pathogenic / LP
0.00
pLI score
1
Active trials
Clinical Summary— PDSS2
🧬
Gene-Disease Validity (ClinGen)
Leigh syndrome · ARModerate

Moderate evidence — consider for supplementary testing

⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
26 Pathogenic / Likely Pathogenic· 141 VUS of 312 total submissions
💊
Clinical Trials
1 active or recruiting trial — potential therapeutic options may be available

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.
1.13LOEUF
pLI 0.000
Z-score 1.12
OE 0.72 (0.48–1.13)
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.
0.47Z-score
OE missense 0.91 (0.81–1.02)
196 obs / 215.6 exp
Tolerant

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.0.72 (0.48–1.13)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.91 (0.81–1.02)
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.0.89
0≤1.21.6
LoF obs/exp: 14 / 19.3Missense obs/exp: 196 / 215.6Syn Z: 0.81

ClinVar Variant Classifications

312 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic22
Likely Pathogenic4
VUS141
Likely Benign117
Benign17
Conflicting11
22
Pathogenic
4
Likely Pathogenic
141
VUS
117
Likely Benign
17
Benign
11
Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
1
0
21
0
22
Likely Pathogenic
3
1
0
0
4
VUS
2
114
23
2
141
Likely Benign
0
2
48
67
117
Benign
0
2
15
0
17
Conflicting
—11
Total611910769312

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

View in ClinVar →

Protein Context — Lollipop Plot

PDSS2 · protein map & ClinVar variants

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

Gene2Phenotype Curations

PDSS2-related coenzyme Q10 deficiency, primary

definitive
ARLoss Of FunctionAbsent Gene Product
Dev. Disorders
G2P ↗

Gene2Phenotype curations · DECIPHER consortium patient cohort (public variants) · deciphergenomics.org

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM

Coenzyme Q10 deficiency, primary, 3

MIM #614652

Molecular basis of disorder known

Autosomal recessive
📖
GeneReview available — PDSS2
Authoritative clinical overview · NCBI Bookshelf · Recommended first read
Open GeneReview ↗
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Genetic susceptibility to caffeine intake and metabolism: a systematic review.
Low JJ et al.·J Transl Med
2024Review
Opicapone for Parkinson's disease-related sleep disturbances: The OASIS clinical trial.
Ferreira JJ et al.·J Parkinsons Dis
2025Clinical trial
Human CoQ10 deficiencies.
Quinzii CM et al.·Biofactors
2008
PDSS2-Del2, a new variant of PDSS2, promotes tumor cell metastasis and angiogenesis in hepatocellular carcinoma via activating NF-κB.
Zeng T et al.·Mol Oncol
2020
The role of NRF2 function and regulation in atherosclerosis: an update.
Dabravolski SA et al.·Mol Cell Biochem
2025Review
Sp1 Mediates the Constitutive Expression and Repression of the PDSS2 Gene in Lung Cancer Cells.
Hu L et al.·Genes (Basel)
2019
Clinical utility of PDSS2 expression to stratify patients at risk for recurrence of hepatocellular carcinoma.
Kanda M et al.·Int J Oncol
2014Cohort
Decrease of PDSS2 expression, a novel tumor suppressor, in non-small cell lung cancer.
Chen P et al.·Cancer Epidemiol
2013
Coenzyme Q(10) deficiency disrupts lipid metabolism by altering cholesterol homeostasis in neurons.
Pesini A et al.·Free Radic Biol Med
2025
Genetic bases and clinical manifestations of coenzyme Q10 (CoQ 10) deficiency.
Desbats MA et al.·J Inherit Metab Dis
2015Review
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov
PARKINSON DISEASE (Disorder)Multiple Sclerosis (MS) - Relapsing-remittingPediatric Patients Affected by Neuromuscolar and Degenerative Diseases

Myrosinase Bioactivated Gglucoraphanin for the Treatment of Neurodegenerative Diseases (GRA-MYR-ND)

RECRUITING
NCT07360977Phase NAIRCCS Centro Neurolesi Bonino PulejoStarted 2026-01
bioactivated GRA for adult patientsbioactivated GRA for pediatric patients

External Resources

Links to major genomics databases and tools