coenzyme Q10 deficiency, primary, 3
diseaseOn this page
Also known as coenzyme Q10 deficiency caused by mutation in PDSS2coenzyme Q10 deficiency, primary, type 3COQ10D3PDSS2 coenzyme Q10 deficiency
Summary
coenzyme Q10 deficiency, primary, 3 (MONDO:0013838) is a disease caused by PDSS2 (GenCC Definitive), with 1 cohort gene.
At a glance
- Causal gene: PDSS2 (GenCC Definitive)
- Cohort genes: 1
- ClinVar variants: 61
Clinical features
No curated clinical features (Orphanet) for this disease.
Identifiers
Disease identifiers
| Field | Value |
|---|---|
| Canonical name | coenzyme Q10 deficiency, primary, 3 |
| Mondo ID | MONDO:0013838 |
| OMIM | 614652 |
| DOID | DOID:0070240 |
| UMLS | C3553358 |
| MedGen | 766272 |
| GARD | 0018379 |
| Is cancer (heuristic) | no |
Also known as: coenzyme Q10 deficiency caused by mutation in PDSS2 · coenzyme Q10 deficiency, primary, 3 · coenzyme Q10 deficiency, primary, type 3 · COQ10D3 · PDSS2 coenzyme Q10 deficiency
Data availability: 61 ClinVar variants · 3 GenCC gene-disease records.
Disease family
Classification path: disease › human disease › disease by developmental or physiological process › metabolic disease › developmental anomaly of metabolic origin › inborn mitochondrial metabolism disorder › mitochondrial oxidative phosphorylation disorder › coenzyme Q10 deficiency › coenzyme Q10 deficiency, primary, 3
Related subtypes (8): coenzyme Q10 deficiency, primary, 1, autosomal recessive ataxia due to ubiquinone deficiency, familial steroid-resistant nephrotic syndrome with sensorineural deafness, deafness-encephaloneuropathy-obesity-valvulopathy syndrome, encephalopathy-hypertrophic cardiomyopathy-renal tubular disease syndrome, neonatal encephalomyopathy-cardiomyopathy-respiratory distress syndrome, primary coenzyme Q10 deficiency 8, coenzyme q10 deficiency, primary, 9
Genetics & variants
GWAS landscape
No GWAS associations recorded — common-variant (GWAS) studies don’t cover this disease (typical for Mendelian / rare diseases). See the curated gene cohort and Mendelian overlap below.
Variant details and genetic-evidence tiers
ClinVar germline variants
61 retrieved; paginated sample, class counts are floors:
39 uncertain significance, 8 conflicting classifications of pathogenicity, 6 likely benign, 3 benign/likely benign, 3 likely pathogenic, 1 pathogenic, 1 benign
| ClinVar | Variant (HGVS) | Gene | Classification | Review |
|---|---|---|---|---|
| 1200 | NM_020381.4(PDSS2):c.964C>T (p.Gln322Ter) | PDSS2 | Pathogenic | no assertion criteria provided |
| 3592875 | NM_020381.4(PDSS2):c.401_402del (p.Asn134fs) | PDSS2 | Likely pathogenic | criteria provided, single submitter |
| 3592877 | NM_020381.4(PDSS2):c.183dup (p.Tyr62fs) | PDSS2 | Likely pathogenic | criteria provided, single submitter |
| 3592878 | NM_020381.4(PDSS2):c.129dup (p.Lys44fs) | PDSS2 | Likely pathogenic | criteria provided, single submitter |
| 1201 | NM_020381.4(PDSS2):c.1145C>T (p.Ser382Leu) | PDSS2 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 1432907 | NM_020381.4(PDSS2):c.1003G>A (p.Gly335Arg) | PDSS2 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 1954682 | NM_020381.4(PDSS2):c.1042-1G>A | PDSS2 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 214987 | NM_020381.4(PDSS2):c.667G>A (p.Val223Ile) | PDSS2 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 214988 | NM_020381.4(PDSS2):c.700A>G (p.Lys234Glu) | PDSS2 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 214989 | NM_020381.4(PDSS2):c.1046G>A (p.Arg349Gln) | PDSS2 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 214991 | NM_020381.4(PDSS2):c.275A>C (p.His92Pro) | PDSS2 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 2174415 | NM_020381.4(PDSS2):c.1045C>T (p.Arg349Ter) | PDSS2 | Conflicting classifications of pathogenicity | criteria provided, conflicting classifications |
| 1030705 | NM_020381.4(PDSS2):c.1151C>A (p.Ala384Asp) | PDSS2 | Uncertain significance | criteria provided, single submitter |
| 1032839 | NM_020381.4(PDSS2):c.837G>A (p.Met279Ile) | PDSS2 | Uncertain significance | criteria provided, single submitter |
| 1430741 | NM_020381.4(PDSS2):c.382G>A (p.Val128Met) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 1440087 | NM_020381.4(PDSS2):c.488G>A (p.Arg163His) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 1481116 | NM_020381.4(PDSS2):c.500A>G (p.Asn167Ser) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 1487136 | NM_020381.4(PDSS2):c.50C>T (p.Ser17Leu) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 1490204 | NM_020381.4(PDSS2):c.737C>T (p.Thr246Ile) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 1498538 | NM_020381.4(PDSS2):c.1096C>T (p.Arg366Cys) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 1498723 | NM_020381.4(PDSS2):c.602A>G (p.Asn201Ser) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 1508923 | NM_020381.4(PDSS2):c.277C>T (p.Pro93Ser) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 1902462 | NM_020381.4(PDSS2):c.76T>G (p.Ser26Ala) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 1919824 | NM_020381.4(PDSS2):c.526G>C (p.Gly176Arg) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 1985939 | NM_020381.4(PDSS2):c.538G>C (p.Asp180His) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 2040436 | NM_020381.4(PDSS2):c.740G>A (p.Trp247Ter) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 2059878 | NM_020381.4(PDSS2):c.1044G>T (p.Leu348Phe) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 2415087 | NM_020381.4(PDSS2):c.1154G>C (p.Arg385Thr) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
| 2434640 | NM_020381.4(PDSS2):c.1070G>T (p.Gly357Val) | PDSS2 | Uncertain significance | criteria provided, single submitter |
| 2462619 | NM_020381.4(PDSS2):c.410T>C (p.Met137Thr) | PDSS2 | Uncertain significance | criteria provided, multiple submitters, no conflicts |
Genes & proteins
Mendelian disease overlap and somatic drivers
GenCC: 4 · Orphanet: 0 · OMIM-shared: 0 · Dual-evidence (GWAS+Mendelian): 0
GenCC gene–disease validity (cohort genes)
the Disease column is the GenCC-asserted condition — a cohort gene’s strongest validity may be for a related predisposition syndrome.
| Gene | Classification | Inheritance | Disease | Records |
|---|---|---|---|---|
| PDSS2 | Definitive | Autosomal recessive | coenzyme Q10 deficiency, primary, 3 | 4 |
Cohort genes → proteins
1 cohort genes, 1 distinct canonical proteins.
Evidence partition
| Subset | Genes |
|---|---|
| multi_evidence | 1 |
Cohort genes (full)
| Symbol | HGNC | Ensembl | UniProt | Name | Evidence |
|---|---|---|---|---|---|
| PDSS2 | HGNC:23041 | ENSG00000164494 | Q86YH6 | All trans-polyprenyl-diphosphate synthase PDSS2 | gencc,clinvar |
Cohort function summary
Lead sentence per gene, UniProt-curated.
| Symbol | Protein name | Function (lead sentence) |
|---|---|---|
| PDSS2 | All trans-polyprenyl-diphosphate synthase PDSS2 | Heterotetrameric enzyme that catalyzes the condensation of farnesyl diphosphate (FPP), which acts as a primer, and isopentenyl diphosphate (IPP) to produce prenyl diphosphates of varying chain lengths and participates in the determination… |
Protein-family classification
Druggable: 1 · Difficult: 0 · Unknown: 0 · Druggable fraction: 1.0
Family distribution
Cohort families vs a genome-wide background (hypergeometric, BH-FDR; fold = observed/expected). Counts kept; sorted by enrichment, so the catch-all Other/Unknown bucket no longer leads.
| Family | Genes | Fold | FDR |
|---|---|---|---|
| Enzyme (other) | 1 | 12.0× | 0.083 |
Per-gene assignment
| Symbol | Family | Druggable? | EC | InterPro (top 3) |
|---|---|---|---|---|
| PDSS2 | Enzyme (other) | yes | 2.5.1.91 | Polyprenyl_synt, Isoprenoid_synthase_dom_sf |
Expression context
Cohort genes with no expression data: 0.
1 cohort gene are a single-cell marker in ≥1 SCXA experiment.
Breadth distribution (Bgee present_calls)
| Bucket | Genes |
|---|---|
| narrow (1-5 tissues) | 0 |
| moderate (6-20) | 0 |
| broad (>20) | 1 |
| unknown | 0 |
Top tissues across cohort
| Tissue | Cohort genes |
|---|---|
| buccal mucosa cell | 1 |
| nephron tubule | 1 |
| secondary oocyte | 1 |
Per-gene tissue summary (top 30)
| Symbol | Bgee breadth | FANTOM5 breadth | SCXA | Top tissues |
|---|---|---|---|---|
| PDSS2 | 256 | ubiquitous | marker | buccal mucosa cell, nephron tubule, secondary oocyte |
Protein interactions among cohort
Intra-cohort edges: 0.
Hub genes (top 10 by interactor count)
| Symbol | Interactor count |
|---|---|
| PDSS2 | 2,414 |
Structural data
PDB: 0 · AlphaFold-only: 1 · No structure: 0
AlphaFold-only cohort genes (top 30 by pLDDT)
| Symbol | UniProt | pLDDT |
|---|---|---|
| PDSS2 | Q86YH6 | 80.28 |
Function
Pathway analysis
Distinct Reactome pathways touched by cohort: 1. Enrichment computed across 1 evidence-associated genes (1 with Reactome annotation).
Pathways by enrichment
Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.
| Pathway | Cohort genes | Fold | FDR | Sample cohort genes |
|---|---|---|---|---|
| Ubiquinol biosynthesis | 1 | 878.5× | 0.001 | PDSS2 |
GO biological processes by enrichment
Over-representation of cohort genes vs the genome-wide background (hypergeometric test, Benjamini-Hochberg FDR; fold = observed/expected over 1 annotated cohort genes). Counts and members are kept as ground-truth; sorted by enrichment.
| GO term | Cohort genes | Fold | FDR | Sample cohort genes |
|---|---|---|---|---|
| regulation of body fluid levels | 1 | 4213.0× | 9e-04 | PDSS2 |
| isoprenoid biosynthetic process | 1 | 1685.2× | 0.001 | PDSS2 |
| ubiquinone biosynthetic process | 1 | 936.2× | 0.001 | PDSS2 |
| cerebellum development | 1 | 358.6× | 0.003 | PDSS2 |
Therapeutics
Drug target analysis
Approved (phase 4): 0 · Phase ≥3: 0 · Phased (≥1): 0 · Undrugged: 1
Druggability breadth: 0 of 1 evidence-associated genes (0%) have a ChEMBL target (buckets above are over the deeply-mined display cohort).
Top cohort targets by molecule count
| Symbol | Molecules | Max phase |
|---|---|---|
| PDSS2 | 0 | 0 |
Bioactivity and enzyme data
Enzyme cohort genes (≥1 EC): 1.
Cohort enzymes (BRENDA EC)
| Symbol | EC numbers | Names |
|---|---|---|
| PDSS2 | 2.5.1.91 | all-trans-decaprenyl-diphosphate synthase |
Pharmacogenomics
Cohort genes with a PharmGKB record: 1; with CPIC/DPWG dosing guidelines: 0.
No cohort gene has a CPIC/DPWG genotype-guided dosing guideline (PharmGKB).
Chemical tractability of cohort targets
0 approved/phased compounds have measured bioactivity against a cohort gene (and aren’t yet in disease-level trials). This is a research / tractability signal, NOT a therapeutic recommendation — a bioactivity row often reflects off-target or screening binding (e.g. promiscuous kinase inhibitors against a cohort kinase), implying no disease mechanism.
Druggability pyramid
Cohort genes binned by druggability tier (high → low):
| Tier | Definition | Genes | Symbols |
|---|---|---|---|
| A | Approved (phase 4 drug) | 0 | |
| B | Phased (≥1) drug, not yet approved | 0 | |
| C | Druggable family + PDB, no drug | 0 | |
| D | Druggable family + AlphaFold only, no drug | 1 | PDSS2 |
| E | Difficult family or no structure, no drug | 0 |
Undrugged target profiles
1 cohort genes are undrugged. Ranked by ‘starting-point quality’ (assay depth + drugged-partner adjacency).
| Symbol | ChEMBL assays | Drugged partners (top 3) |
|---|---|---|
| PDSS2 | 0 | — |
Clinical trials & evidence
Clinical trials
Clinical trials: 0.
Related Atlas pages
- Cohort genes: PDSS2